diff --git a/CMake/BuildConfigurations/camiPhotoacousticsWorkstation.cmake b/CMake/BuildConfigurations/camiPhotoacousticsWorkstation.cmake new file mode 100644 index 0000000000..14a6e49fd8 --- /dev/null +++ b/CMake/BuildConfigurations/camiPhotoacousticsWorkstation.cmake @@ -0,0 +1,21 @@ +message(STATUS "Configuring MITK Photoacoustics Setup Build") + +# Enable open cv and open igt link, which is a necessary configuration +set(MITK_USE_OpenCV ON CACHE BOOL "MITK Use OpenCV Library" FORCE) +set(MITK_USE_OpenIGTLink ON CACHE BOOL "MITK Use OpenIGTLink Library" FORCE) + +set(MITK_USE_OpenCL ON CACHE BOOL "MITK Use OpenCL Library" FORCE) + +# Enable default plugins and the navigation modules +set(MITK_CONFIG_PLUGINS + org.mitk.gui.qt.datamanager + org.mitk.gui.qt.stdmultiwidgeteditor + org.mitk.gui.qt.imagenavigator + org.mitk.gui.qt.properties + org.mitk.gui.qt.viewnavigator + org.mitk.gui.qt.ultrasound + org.mitk.gui.qt.photoacoustics.imageprocessing + org.mitk.gui.qt.measurementtoolbox + org.mitk.gui.qt.pointsetinteraction +) + diff --git a/CMake/FindOpenCL.cmake b/CMake/FindOpenCL.cmake index e30fb7a484..848594e9e3 100644 --- a/CMake/FindOpenCL.cmake +++ b/CMake/FindOpenCL.cmake @@ -1,89 +1,88 @@ # - Try to find OpenCL # This module tries to find an OpenCL implementation on your system. It supports # AMD / ATI, Apple and NVIDIA implementations, but should work, too. # # To set manually the paths, define these environment variables: # OpenCL_INCPATH - Include path (e.g. OpenCL_INCPATH=/opt/cuda/4.0/cuda/include) # OpenCL_LIBPATH - Library path (e.h. OpenCL_LIBPATH=/usr/lib64/nvidia) # # Once done this will define # OPENCL_FOUND - system has OpenCL # OPENCL_INCLUDE_DIRS - the OpenCL include directory # OPENCL_LIBRARIES - link these to use OpenCL # # WIN32 should work, but is untested FIND_PACKAGE(PackageHandleStandardArgs) SET (OPENCL_VERSION_STRING "0.1.0") SET(OPENCL_VERSION_MAJOR 0) SET(OPENCL_VERSION_MINOR 1) SET(OPENCL_VERSION_PATCH 0) IF(APPLE) FIND_LIBRARY(OPENCL_LIBRARIES OpenCL DOC "OpenCL lib for OSX") FIND_PATH(OPENCL_INCLUDE_DIRS OpenCL/cl.h DOC "Include for OpenCL on OSX") FIND_PATH(_OPENCL_CPP_INCLUDE_DIRS OpenCL/cl.hpp DOC "Include for OpenCL CPP bindings on OSX") ELSE() IF (WIN32) FIND_PATH(OPENCL_INCLUDE_DIRS CL/cl.h) FIND_PATH(_OPENCL_CPP_INCLUDE_DIRS CL/cl.hpp) IF(CMAKE_SIZEOF_VOID_P MATCHES "8") SET(OPENCL_LIB_DIR "$ENV{ATISTREAMSDKROOT}/lib/x86_64") if(NOT IS_DIRECTORY ${OPENCL_LIB_DIR}) SET(OPENCL_LIB_DIR "$ENV{CUDA_PATH}/lib/x64") endif() ELSE() SET(OPENCL_LIB_DIR "$ENV{ATISTREAMSDKROOT}/lib/x86") if(NOT IS_DIRECTORY ${OPENCL_LIB_DIR}) # need to convert path in the cmake style ? SET(OPENCL_LIB_DIR "$ENV{CUDA_PATH}/lib/Win32") endif() ENDIF() file(TO_CMAKE_PATH ${OPENCL_LIB_DIR} OPENCL_LIB_DIR) GET_FILENAME_COMPONENT(OPENCL_LIB_DIR ${OPENCL_LIB_DIR} ABSOLUTE) FIND_LIBRARY(OPENCL_LIBRARIES OpenCL.lib PATHS ${OPENCL_LIB_DIR} ENV OpenCL_LIBPATH) GET_FILENAME_COMPONENT(_OPENCL_INC_CAND ${OPENCL_LIB_DIR}/../../include ABSOLUTE) # On Win32 search relative to the library FIND_PATH(OPENCL_INCLUDE_DIRS CL/cl.h PATHS "${_OPENCL_INC_CAND}" ENV OpenCL_INCPATH) FIND_PATH(_OPENCL_CPP_INCLUDE_DIRS CL/cl.hpp PATHS "${_OPENCL_INC_CAND}" ENV OpenCL_INCPATH) - ELSE (WIN32) + ELSE () # Unix style platforms - FIND_LIBRARY(OPENCL_LIBRARIES OpenCL - PATHS ENV LD_LIBRARY_PATH ENV OpenCL_LIBPATH + FIND_LIBRARY(OPENCL_LIBRARIES libOpenCL.so + PATHS "/usr/local/cuda/lib64" "/opt/AMDAPP/lib64" ENV LD_LIBRARY_PATH ENV OpenCL_LIBPATH ) - GET_FILENAME_COMPONENT(OPENCL_LIB_DIR ${OPENCL_LIBRARIES} PATH) GET_FILENAME_COMPONENT(_OPENCL_INC_CAND ${OPENCL_LIB_DIR}/../../include ABSOLUTE) # The AMD SDK currently does not place its headers # in /usr/include, therefore also search relative # to the library FIND_PATH(OPENCL_INCLUDE_DIRS CL/cl.h PATHS ${_OPENCL_INC_CAND} "/usr/local/cuda/include" "/opt/AMDAPP/include" ENV OpenCL_INCPATH) FIND_PATH(_OPENCL_CPP_INCLUDE_DIRS CL/cl.hpp PATHS ${_OPENCL_INC_CAND} "/usr/local/cuda/include" "/opt/AMDAPP/include" ENV OpenCL_INCPATH) - ENDIF (WIN32) + ENDIF () -ENDIF (APPLE) +ENDIF () FIND_PACKAGE_HANDLE_STANDARD_ARGS(OpenCL DEFAULT_MSG OPENCL_LIBRARIES OPENCL_INCLUDE_DIRS) IF(_OPENCL_CPP_INCLUDE_DIRS) SET( OPENCL_HAS_CPP_BINDINGS TRUE ) LIST( APPEND OPENCL_INCLUDE_DIRS ${_OPENCL_CPP_INCLUDE_DIRS} ) # This is often the same, so clean up LIST( REMOVE_DUPLICATES OPENCL_INCLUDE_DIRS ) ENDIF(_OPENCL_CPP_INCLUDE_DIRS) MARK_AS_ADVANCED( OPENCL_INCLUDE_DIRS ) diff --git a/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox b/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox index 13d05fa1af..67ac20c7c5 100644 --- a/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox +++ b/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox @@ -1,67 +1,68 @@ /** \page PluginListPage MITK Plugin Manuals \section PluginListPageOverview Overview The plugins and bundles provide much of the extended functionality of MITK. Each encapsulates a solution to a problem and associated features. This way one can easily assemble the necessary capabilites for a workflow without adding a lot of bloat, by combining plugins as needed. The distinction between developer and end user use is for convenience only and mainly distinguishes which group a plugin is primarily aimed at. \section PluginListPageEndUserPluginList List of Plugins for End User Use \li \subpage org_blueberry_ui_qt_log \li \subpage org_mitk_views_basicimageprocessing \li \subpage org_mitk_views_cmdlinemodules \li \subpage org_mitk_views_datamanager \li \subpage org_mitk_gui_qt_dicom \li \subpage org_mitk_gui_qt_dicominspector \li \subpage org_mitk_gui_qt_diffusionimaging \li \subpage org_mitk_gui_qt_imagecropper \li \subpage org_mitk_views_imagenavigator \li \subpage org_mitk_gui_qt_measurementtoolbox \li \subpage org_mitk_gui_qt_moviemaker \li \subpage org_mitk_views_screenshotmaker + \li \subpage org_mitk_gui_qt_photoacoustics_imageprocessing \li \subpage org_mitk_views_pointsetinteraction \li \subpage org_mitk_gui_qt_pointsetinteractionmultispectrum \li \subpage org_mitk_gui_qt_python \li \subpage org_mitk_gui_qt_remeshing \li \subpage org_mitk_views_segmentation \li \subpage org_mitk_views_multilabelsegmentation \li \subpage org_mitk_gui_qt_spectrocamrecorder \li \subpage org_mitk_gui_qt_ultrasound \li \subpage org_mitk_gui_qt_viewnavigator \li \subpage org_mitk_views_volumevisualization \li \subpage org_mitk_gui_qt_xnat \li \subpage org_mitk_gui_qt_aicpregistration \li \subpage org_mitk_gui_qt_igtlplugin \li \subpage org_mitk_gui_qt_geometrytools \li \subpage org_mitk_gui_qt_classificationsegmentation \li \subpage org_mitk_gui_qt_matchpoint_algorithm_batch \li \subpage org_mitk_gui_qt_matchpoint_algorithm_browser \li \subpage org_mitk_gui_qt_matchpoint_algorithm_control \li \subpage org_mitk_gui_qt_matchpoint_evaluator \li \subpage org_mitk_gui_qt_matchpoint_framereg \li \subpage org_mitk_gui_qt_matchpoint_manipulator \li \subpage org_mitk_gui_qt_matchpoint_mapper \li \subpage org_mitk_gui_qt_matchpoint_visualizer \li \subpage org_mitk_gui_qt_cest \section PluginListPageDevPluginList List of Plugins for Developer Use and Examples \li \subpage org_surfacematerialeditor \li \subpage org_toftutorial \li \subpage org_mitk_gui_qt_examples \li \subpage org_mitkexamplesopencv \li \subpage org_mitk_gui_qt_igtexample \li \subpage org_mitk_gui_qt_igttracking \li \subpage org_mitk_gui_qt_igt_app_echotrack \li \subpage org_blueberry_ui_qt_objectinspector \li \subpage org_mitk_gui_qt_eventrecorder \li \subpage org_mitk_gui_qt_overlaymanager \li \subpage org_mitk_example_gui_pcaexample \li \subpage org_mitk_gui_qt_renderwindowmanager \li \subpage org_mitk_gui_qt_lasercontrol \li \subpage org_mitk_gui_qt_photoacoustics_imageprocessing \li \subpage org_mitk_gui_qt_lasercontrol \li \subpage org_mitk_gui_qt_igttrackingsemiautomaticmeasurement */ diff --git a/Documentation/Doxygen/3-DeveloperManual/Toolkit/ModuleManuals/MITKModuleManualsList.dox b/Documentation/Doxygen/3-DeveloperManual/Toolkit/ModuleManuals/MITKModuleManualsList.dox index 204dd984fd..3d18e0605d 100644 --- a/Documentation/Doxygen/3-DeveloperManual/Toolkit/ModuleManuals/MITKModuleManualsList.dox +++ b/Documentation/Doxygen/3-DeveloperManual/Toolkit/ModuleManuals/MITKModuleManualsList.dox @@ -1,30 +1,31 @@ /** \page MITKModuleManualsListPage MITK Module Manuals \section MITKModuleManualsListPageOverview Overview The modules are shared libraries that provide functionality that can be used by developers. \section MITKModuleManualsListPageModuleManualList List of Module Manuals \li \subpage NavigationGeneralModulePage \li \subpage MitkOpenCL_Overview \li \subpage LegacyGLModule \li \subpage GeneratingDeviceModulesPage \li \subpage mitkPython_Overview \li \subpage USModulePage + \li \subpage PAModulePage \li \subpage AnnotationModulePage \li \subpage ChartModule \section MITKModuleManualsListPageAdditionalInformation Additional Information on Certain Modules \li \ref PlanarPropertiesPage \li \subpage DiffusionImagingPropertiesPage \li \subpage ConnectomicsRenderingPropertiesPage \section MITKMigrationGuides Migration Guides \li \subpage InteractionMigration \li \subpage GeometryMigration \li \subpage OverlayMigration */ diff --git a/Modules/OpenCL/files.cmake b/Modules/OpenCL/files.cmake index 799077854e..c1f158a404 100644 --- a/Modules/OpenCL/files.cmake +++ b/Modules/OpenCL/files.cmake @@ -1,23 +1,26 @@ set(CPP_FILES # helper classes mitkOclUtils.cpp mitkOclResourceServiceImpl_Private.cpp mitkOclImageFormats.cpp # module activator mitkOpenCLActivator.cpp # base data and filter objects mitkOclBaseData.cpp mitkOclImage.cpp + mitkOclDataSet.cpp mitkOclFilter.cpp mitkOclImageFilter.cpp + mitkOclDataSetFilter.cpp mitkOclImageToImageFilter.cpp + mitkOclDataSetToDataSetFilter.cpp # own filter implementations mitkOclBinaryThresholdImageFilter.cpp ) set(RESOURCE_FILES BinaryThresholdFilter.cl ) diff --git a/Modules/OpenCL/mitkOclDataSet.cpp b/Modules/OpenCL/mitkOclDataSet.cpp new file mode 100644 index 0000000000..953c0d68b1 --- /dev/null +++ b/Modules/OpenCL/mitkOclDataSet.cpp @@ -0,0 +1,176 @@ +/*=================================================================== + +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 "mitkOclDataSet.h" +#include "mitkCommon.h" +#include "mitkLogMacros.h" + +#include "mitkOclUtils.h" + +#include + +//#define SHOW_MEM_INFO + +mitk::OclDataSet::OclDataSet() : m_gpuBuffer(nullptr), m_context(nullptr), m_bufferSize(0), m_gpuModified(false), m_cpuModified(false), + m_Data(nullptr), m_BpE(1) +{ +} + +mitk::OclDataSet::~OclDataSet() +{ + MITK_DEBUG << "OclDataSet Destructor"; + + //release GMEM Image buffer + if (m_gpuBuffer) clReleaseMemObject(m_gpuBuffer); +} + + +cl_mem mitk::OclDataSet::CreateGPUBuffer() +{ + MITK_DEBUG << "InitializeGPUBuffer call with: BPE=" << m_BpE; + + us::ServiceReference ref = GetModuleContext()->GetServiceReference(); + OclResourceService* resources = GetModuleContext()->GetService(ref); + + m_context = resources->GetContext(); + + int clErr; + if (m_gpuBuffer) clReleaseMemObject(m_gpuBuffer); + + m_gpuBuffer = clCreateBuffer(m_context, CL_MEM_READ_WRITE, m_bufferSize * (size_t)m_BpE, nullptr, &clErr); + + #ifdef SHOW_MEM_INFO + MITK_INFO << "Created GPU Buffer Object of size: " << (size_t)m_BpE * m_bufferSize << " Bytes"; + #endif + + CHECK_OCL_ERR(clErr); + + if (clErr != CL_SUCCESS) + mitkThrow() << "openCL Error when creating Buffer"; + + return m_gpuBuffer; +} + +bool mitk::OclDataSet::IsModified(int _type) +{ + if (_type) return m_cpuModified; + else return m_gpuModified; +} + +void mitk::OclDataSet::Modified(int _type) +{ + // defines... GPU: 0, CPU: 1 + m_cpuModified = _type; + m_gpuModified = !_type; +} + +int mitk::OclDataSet::TransferDataToGPU(cl_command_queue gpuComQueue) +{ + cl_int clErr = 0; + + // check whether an image present + if (m_Data == nullptr){ + MITK_ERROR("ocl.DataSet") << "(mitk) No data present!\n"; + return -1; + } + + // there is a need for copy only if RAM-Data newer then GMEM data + if (m_cpuModified) + { + //check the buffer + if(m_gpuBuffer == nullptr) + { + CreateGPUBuffer(); + } + + if (m_gpuBuffer != nullptr) + { + clErr = clEnqueueWriteBuffer(gpuComQueue, m_gpuBuffer, CL_TRUE, 0, m_bufferSize * (size_t)m_BpE, m_Data, 0, NULL, NULL); + MITK_DEBUG << "Wrote Data to GPU Buffer Object."; + + CHECK_OCL_ERR(clErr); + m_gpuModified = true; + + if (clErr != CL_SUCCESS) + mitkThrow() << "openCL Error when writing Buffer"; + } + else + { + MITK_ERROR << "No GPU buffer present!"; + } + } + + return clErr; +} + +cl_mem mitk::OclDataSet::GetGPUBuffer() +{ + // query image object info only if already initialized + if( this->m_gpuBuffer ) + { + #ifdef SHOW_MEM_INFO + cl_int clErr = 0; + // clGetMemObjectInfo() + cl_mem_object_type memInfo; + clErr = clGetMemObjectInfo(this->m_gpuBuffer, CL_MEM_TYPE, sizeof(cl_mem_object_type), &memInfo, nullptr ); + CHECK_OCL_ERR(clErr); + MITK_DEBUG << "Querying info for object, recieving: " << memInfo; + #endif + } + + return m_gpuBuffer; +} + +void* mitk::OclDataSet::TransferDataToCPU(cl_command_queue gpuComQueue) +{ + cl_int clErr = 0; + + // if image created on GPU, needs to create mitk::Image + if( m_gpuBuffer == nullptr ){ + MITK_ERROR("ocl.DataSet") << "(mitk) No buffer present!\n"; + return nullptr; + } + + // check buffersize + char* data = new char[m_bufferSize * (size_t)m_BpE]; + + // debug info + #ifdef SHOW_MEM_INFO + oclPrintMemObjectInfo( m_gpuBuffer ); + #endif + + clErr = clEnqueueReadBuffer( gpuComQueue, m_gpuBuffer, CL_TRUE, 0, m_bufferSize * (size_t)m_BpE, data ,0, nullptr, nullptr); + CHECK_OCL_ERR(clErr); + + if(clErr != CL_SUCCESS) + mitkThrow() << "openCL Error when reading Output Buffer"; + + clFlush( gpuComQueue ); + // the cpu data is same as gpu + this->m_gpuModified = false; + + return (void*) data; +} + +void mitk::OclDataSet::SetBufferSize(size_t size) +{ + m_bufferSize = size; +} + +void mitk::OclDataSet::SetBpE(unsigned short BpE) +{ + m_BpE = BpE; +} diff --git a/Modules/OpenCL/mitkOclDataSet.h b/Modules/OpenCL/mitkOclDataSet.h new file mode 100644 index 0000000000..773510e47c --- /dev/null +++ b/Modules/OpenCL/mitkOclDataSet.h @@ -0,0 +1,134 @@ +/*=================================================================== + +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 __mitkOclDataSet_h +#define __mitkOclDataSet_h + +#define GPU_DATA 0 +#define CPU_DATA 1 + +#include +#include "MitkOpenCLExports.h" + +#include "mitkOclBaseData.h" +#include "mitkOpenCLActivator.h" + +#include + +namespace mitk { + +/*! + * \brief Class implementing processing of arbitrary data sets for GPU Image Processing + * + * The class holds a pointer to the data stored in RAM and performs an + * on-demand-copy to the graphics memory. It is the basic data structure for all + * mitk::oclDataSetToDataSetFilter classes + */ +class MITKOPENCL_EXPORT OclDataSet : public OclBaseData +{ +public: + mitkClassMacro(OclDataSet, OclBaseData); + itkFactorylessNewMacro(Self) + itkCloneMacro(Self) + + /*! \brief Copies the RAM-stored data to GMEM */ + virtual int TransferDataToGPU(cl_command_queue); + + /*! \brief Copies the in GMEM stored data to RAM */ + virtual void* TransferDataToCPU(cl_command_queue); + + /*! \brief Returns the pointer to the referenced data */ + void* GetData() + { + return m_Data; + } + + /** Returns the pointer to the GPU buffer */ + cl_mem GetGPUBuffer(); + + /** Create the GPU buffer for image + * + */ + cl_mem CreateGPUBuffer(); + + /** \brief Returns the status of the image buffer + * + * @param _type The flag to specify the buffer type ( GPU / CPU ) + */ + bool IsModified(int _type); + + using OclBaseData::Modified; + + /** \brief Set the modified flag for one of the buffers + * + * @param _type The flag to specify the buffer type ( GPU / CPU ) + */ + void Modified(int _type); + + /** \brief Initialze the OclDataSet with data. */ + void SetData(void* data) + { + this->m_cpuModified = true; + this->m_gpuModified = false; + m_Data = data; + } + + /*! \brief returns the amount of elements in the DataSet */ + size_t GetBufferSize() const + { + return this->m_bufferSize; + } + + short GetBytesPerElement() const + { + return this->m_BpE; + } + + /** @brief Set the amount of elements in buffer*/ + void SetBufferSize(size_t size); + + /** @brief Set the DataSet memory Size per Element in Bytes*/ + void SetBpE(unsigned short BpE); + +protected: + /*! \brief Constructor */ + OclDataSet(); + + /** @brief Destructor */ + virtual ~OclDataSet(); + + /*! GMEM Image buffer */ + cl_mem m_gpuBuffer; + + /*! GPU Context the Buffer was created in, needed for access */ + cl_context m_context; + +private: + /*! GMEM Buffer Size in elements*/ + size_t m_bufferSize; + + bool m_gpuModified; + bool m_cpuModified; + + /*! Reference to the data */ + void* m_Data; + + /*! Bytes per Element in Buffer*/ + unsigned short m_BpE; +}; + +} +#endif //__mitkOclDataSet_h diff --git a/Modules/OpenCL/mitkOclDataSetFilter.cpp b/Modules/OpenCL/mitkOclDataSetFilter.cpp new file mode 100644 index 0000000000..f30719b5ae --- /dev/null +++ b/Modules/OpenCL/mitkOclDataSetFilter.cpp @@ -0,0 +1,55 @@ +/*=================================================================== + +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 "mitkOclDataSetFilter.h" +#include "mitkOclFilter.h" +#include "mitkOclDataSet.h" +#include "mitkImageReadAccessor.h" + +mitk::OclDataSetFilter::OclDataSetFilter() +{ +} + +mitk::OclDataSetFilter::~OclDataSetFilter() +{ +} + +void mitk::OclDataSetFilter::SetInput(mitk::OclDataSet::Pointer DataSet) +{ + m_Input = DataSet; +} + +void mitk::OclDataSetFilter::SetInput(void* DataSet, unsigned int size, unsigned int BpE) +{ + m_Input = mitk::OclDataSet::New(); + m_Input->SetData(DataSet); + m_Input->SetBufferSize(size); + m_Input->SetBpE(BpE); + m_CurrentSize = BpE; +} + +void mitk::OclDataSetFilter::SetInput(mitk::Image::Pointer image) +{ + m_Input = mitk::OclDataSet::New(); + mitk::ImageReadAccessor reader(image); + + m_Input->SetData(const_cast(reader.GetData())); + m_CurrentSize = (unsigned int)(image->GetPixelType().GetBitsPerComponent() / 8); + unsigned int elements = image->GetDimension(0) * image->GetDimension(1) * image->GetDimension(2); + + m_Input->SetBufferSize(elements); + m_Input->SetBpE(m_CurrentSize); +} \ No newline at end of file diff --git a/Modules/OpenCL/mitkOclDataSetFilter.h b/Modules/OpenCL/mitkOclDataSetFilter.h new file mode 100644 index 0000000000..881291bbd0 --- /dev/null +++ b/Modules/OpenCL/mitkOclDataSetFilter.h @@ -0,0 +1,69 @@ +/*=================================================================== + +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 __mitkOclDataSetFilter_h +#define __mitkOclDataSetFilter_h + +#include "mitkOclFilter.h" +#include "mitkOclDataSet.h" + +#define FILTER_UCHAR 0 +#define FILTER_SHORT 1 + +namespace mitk +{ +class OclFilter; +class OclDataSetFilter; + + /** + * \brief The OclDataSetFilter is the topmost class for all filter which take DataSets as input. + * + * The input DataSet can be intialized via an oclDataSet or a pointer to the data + * This makes it possible to create a filter pipeline of GPU-based filters + * and to bind this part into the CPU (ITK) filter pipeline. + */ +class MITKOPENCL_EXPORT OclDataSetFilter: public OclFilter +{ +public: + /** + * @brief SetInput SetInput Set the input DataSet (as mitk::OclDataSet). + * @param DataSet The DataSet in mitk::OclDataSet. + */ + void SetInput(mitk::OclDataSet::Pointer DataSet); + + /** + * @brief SetInput Set the input DataSet (as a pointer to the data). + * @param DataSet The DataSet in mitk::OclDataSet. + */ + void SetInput(void* DataSet, unsigned int size, unsigned int BpE); + + /** + * @brief SetInput Set the input DataSet (as mitk::Image). + * @param DataSet The DataSet in mitk::OclDataSet. + */ + void SetInput(mitk::Image::Pointer image); + +protected: + OclDataSetFilter(); + + virtual ~OclDataSetFilter(); + + /** The input DataSet */ + mitk::OclDataSet::Pointer m_Input; + unsigned int m_CurrentSize; +}; +} +#endif // __mitkOclDataSetFilter_h diff --git a/Modules/OpenCL/mitkOclDataSetToDataSetFilter.cpp b/Modules/OpenCL/mitkOclDataSetToDataSetFilter.cpp new file mode 100644 index 0000000000..2cf7acab5d --- /dev/null +++ b/Modules/OpenCL/mitkOclDataSetToDataSetFilter.cpp @@ -0,0 +1,128 @@ +/*=================================================================== + +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 "mitkOclDataSetToDataSetFilter.h" +#include "mitkOclDataSet.h" + +#include "mitkException.h" + +mitk::OclDataSetToDataSetFilter::OclDataSetToDataSetFilter() +{ + m_Output = mitk::OclDataSet::New(); +} + + +mitk::OclDataSetToDataSetFilter::~OclDataSetToDataSetFilter() +{ +} + +mitk::OclDataSet::Pointer mitk::OclDataSetToDataSetFilter::GetGPUOutput() +{ + return this->m_Output; +} + +void* mitk::OclDataSetToDataSetFilter::GetOutput() +{ + void* pData = m_Output->TransferDataToCPU(m_CommandQue); + return pData; +} + +int mitk::OclDataSetToDataSetFilter::GetBytesPerElem() +{ + return this->m_CurrentSizeOutput; +} + +bool mitk::OclDataSetToDataSetFilter::InitExec(cl_kernel ckKernel, unsigned int* dimensions, size_t outputDataSize, unsigned int outputBpE) +{ + cl_int clErr = 0; + + if (m_Input.IsNull()) + mitkThrow() << "Input DataSet is null."; + + // get DataSet size once + const unsigned int uiDataSetWidth = dimensions[0]; + const unsigned int uiDataSetHeight = dimensions[1]; + const unsigned int uiDataSetDepth = dimensions[2]; + + // compute work sizes + this->SetWorkingSize(8, uiDataSetWidth, 8, uiDataSetHeight, 8, uiDataSetDepth); + + cl_mem clBuffIn = m_Input->GetGPUBuffer(); + cl_mem clBuffOut = m_Output->GetGPUBuffer(); + + if (!clBuffIn) + { + if (m_Input->TransferDataToGPU(m_CommandQue) != CL_SUCCESS) + { + mitkThrow() << "Could not create / initialize gpu DataSet."; + } + + clBuffIn = m_Input->GetGPUBuffer(); + } + + // output DataSet not initialized or output buffer size changed + if (!clBuffOut || (size_t)m_Output->GetBufferSize() != outputDataSize) + { + MITK_DEBUG << "Create GPU DataSet call " << uiDataSetWidth << "x" << uiDataSetHeight << "x" << uiDataSetDepth; + m_Output->SetBpE(outputBpE); + m_Output->SetBufferSize(outputDataSize); + clBuffOut = m_Output->CreateGPUBuffer(); + m_CurrentSizeOutput = outputBpE; + } + + clErr = 0; + clErr = clSetKernelArg(ckKernel, 0, sizeof(cl_mem), &clBuffIn); + clErr |= clSetKernelArg(ckKernel, 1, sizeof(cl_mem), &clBuffOut); + CHECK_OCL_ERR(clErr); + + if (clErr != CL_SUCCESS) + mitkThrow() << "OpenCL Part initialization failed with " << GetOclErrorAsString(clErr); + + return(clErr == CL_SUCCESS); +} + +bool mitk::OclDataSetToDataSetFilter::InitExecNoInput(cl_kernel ckKernel, unsigned int* dimensions, size_t outputDataSize, unsigned int outputBpE) +{ + cl_int clErr = 0; + + // get DataSet size once + const unsigned int uiDataSetWidth = dimensions[0]; + const unsigned int uiDataSetHeight = dimensions[1]; + const unsigned int uiDataSetDepth = dimensions[2]; + + // compute work sizes + this->SetWorkingSize(8, uiDataSetWidth, 8, uiDataSetHeight, 8, uiDataSetDepth); + + cl_mem clBuffOut = m_Output->GetGPUBuffer(); + + // output DataSet not initialized or output buffer size changed + if (!clBuffOut || (size_t)m_Output->GetBufferSize() != outputDataSize) + { + MITK_DEBUG << "Create GPU DataSet call " << uiDataSetWidth << "x" << uiDataSetHeight << "x" << uiDataSetDepth; + m_Output->SetBpE(outputBpE); + m_Output->SetBufferSize(outputDataSize); + clBuffOut = m_Output->CreateGPUBuffer(); + m_CurrentSizeOutput = outputBpE; + } + + clErr = clSetKernelArg(ckKernel, 0, sizeof(cl_mem), &clBuffOut); + CHECK_OCL_ERR(clErr); + + if (clErr != CL_SUCCESS) + mitkThrow() << "OpenCL Part initialization failed with " << GetOclErrorAsString(clErr); + + return(clErr == CL_SUCCESS); +} \ No newline at end of file diff --git a/Modules/OpenCL/mitkOclDataSetToDataSetFilter.h b/Modules/OpenCL/mitkOclDataSetToDataSetFilter.h new file mode 100644 index 0000000000..0891e8b876 --- /dev/null +++ b/Modules/OpenCL/mitkOclDataSetToDataSetFilter.h @@ -0,0 +1,81 @@ +/*=================================================================== + +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 __mitkOclDataSetToDataSetFilter_h +#define __mitkOclDataSetToDataSetFilter_h + +#include "mitkOclDataSetFilter.h" + +namespace mitk +{ +class OclDataSetFilter; +class OclDataSetToDataSetFilter; + +/** @class OclDataSetToDataSetFilter + * @brief The OclDataSetToDataSetFilter is the base class for all OpenCL DataSet filter generating DataSets. + */ +class MITKOPENCL_EXPORT OclDataSetToDataSetFilter: public OclDataSetFilter +{ +public: + /*! + * \brief Returns an pointer to the filtered data. + */ + void* GetOutput(); + + /*! + * \brief Returns a pointer to the graphics memory. + * + * Use this method when executing two and more filters on the GPU for fast access. + * This method does not copy the data to RAM. It returns only a pointer. + */ + mitk::OclDataSet::Pointer GetGPUOutput(); + +protected: + /** + * @brief OclDataSetToDataSetFilter Default constructor. + */ + OclDataSetToDataSetFilter(); + + /** @brief Destructor */ + virtual ~OclDataSetToDataSetFilter(); + + /** Output DataSet */ + mitk::OclDataSet::Pointer m_Output; + + /** @brief (Virtual) method Update() to be implemented in derived classes. */ + virtual void Update() = 0; + + /** + * @brief InitExec Initialize the execution + * @param ckKernel The GPU kernel. + * @throws mitk::Exception if something goes wrong. + * @return True for success. + */ + bool InitExec(cl_kernel ckKernel, unsigned int* dimensions, size_t outputDataSize, unsigned int outputBpE); + + bool InitExecNoInput(cl_kernel ckKernel, unsigned int* dimensions, size_t outputDataSize, unsigned int outputBpE); + + /** @brief Get the memory size needed for each element */ + virtual int GetBytesPerElem(); + + unsigned int m_CurrentSizeOutput; + +private: + /** Block dimensions */ + unsigned int m_BlockDims[3]; +}; +} +#endif // __mitkOclDataSetToDataSetFilter_h diff --git a/Modules/OpenCL/mitkOclFilter.cpp b/Modules/OpenCL/mitkOclFilter.cpp index 5312e59117..a3fb6c9ebd 100644 --- a/Modules/OpenCL/mitkOclFilter.cpp +++ b/Modules/OpenCL/mitkOclFilter.cpp @@ -1,248 +1,355 @@ /*=================================================================== 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. ===================================================================*/ //Ocl #include "mitkOclFilter.h" #include "mitkOclUtils.h" #include "mitkOpenCLActivator.h" + //Mitk #include #include //usService #include "usServiceReference.h" #include #include #include #include #include #include +//standard library +#include + mitk::OclFilter::OclFilter() : m_ClCompilerFlags(""), m_ClProgram(nullptr), m_CommandQue(nullptr), m_FilterID("mitkOclFilter"), m_Preambel(" "), m_Initialized(false) { } mitk::OclFilter::OclFilter(const char* filename) : m_ClCompilerFlags(""), m_ClProgram(nullptr), m_CommandQue(nullptr), m_FilterID(filename), m_Preambel(" "), m_Initialized(false) { m_ClFiles.push_back(filename); } mitk::OclFilter::~OclFilter() { MITK_DEBUG << "OclFilter Destructor"; // release program if (m_ClProgram) { us::ServiceReference ref = GetModuleContext()->GetServiceReference(); OclResourceService* resources = GetModuleContext()->GetService(ref); // remove program from storage resources->RemoveProgram(m_FilterID); } } bool mitk::OclFilter::ExecuteKernel( cl_kernel kernel, unsigned int workSizeDim ) { cl_int clErr = 0; clErr = clEnqueueNDRangeKernel( this->m_CommandQue, kernel, workSizeDim, nullptr, this->m_GlobalWorkSize, m_LocalWorkSize, 0, nullptr, nullptr); CHECK_OCL_ERR( clErr ); return ( clErr == CL_SUCCESS ); } +bool mitk::OclFilter::ExecuteKernelChunks( cl_kernel kernel, unsigned int workSizeDim, size_t* chunksDim ) +{ + size_t offset[3] ={0, 0, 0}; + cl_int clErr = 0; + + if(workSizeDim == 2) + { + for(offset[0] = 0; offset[0] < m_GlobalWorkSize[0]; offset[0] += chunksDim[0]) + { + for(offset[1] = 0; offset[1] < m_GlobalWorkSize[1]; offset[1] += chunksDim[1]) + { + clErr |= clEnqueueNDRangeKernel(this->m_CommandQue, kernel, workSizeDim, + offset, chunksDim, m_LocalWorkSize, 0, nullptr, nullptr); + } + } + } + else if(workSizeDim == 3) + { + for(offset[0] = 0; offset[0] < m_GlobalWorkSize[0]; offset[0] += chunksDim[0]) + { + for(offset[1] = 0; offset[1] < m_GlobalWorkSize[1]; offset[1] += chunksDim[1]) + { + for(offset[2] = 0; offset[2] < m_GlobalWorkSize[2]; offset[2] += chunksDim[2]) + { + clErr |= clEnqueueNDRangeKernel( this->m_CommandQue, kernel, workSizeDim, + offset, chunksDim, m_LocalWorkSize, 0, nullptr, nullptr); + } + } + } + } + + CHECK_OCL_ERR(clErr); + + return ( clErr == CL_SUCCESS ); +} + +bool mitk::OclFilter::ExecuteKernelChunksInBatches(cl_kernel kernel, unsigned int workSizeDim, size_t* chunksDim, size_t batchSize, int waitTimems) +{ + size_t offset[3] = { 0, 0, 0 }; + cl_int clErr = 0; + + unsigned int currentChunk = 0; + cl_event* waitFor = new cl_event[batchSize]; + + if (workSizeDim == 2) + { + for (offset[0] = 0; offset[0] < m_GlobalWorkSize[0]; offset[0] += chunksDim[0]) + { + for (offset[1] = 0; offset[1] < m_GlobalWorkSize[1]; offset[1] += chunksDim[1]) + { + if (currentChunk % batchSize == 0 && currentChunk != 0) + { + clWaitForEvents(batchSize, &waitFor[0]); + std::this_thread::sleep_for(std::chrono::milliseconds(waitTimems)); + clErr |= clEnqueueNDRangeKernel(this->m_CommandQue, kernel, workSizeDim, + offset, chunksDim, m_LocalWorkSize, 0, nullptr, &waitFor[0]); + } + else + { + clErr |= clEnqueueNDRangeKernel(this->m_CommandQue, kernel, workSizeDim, + offset, chunksDim, m_LocalWorkSize, 0, nullptr, &waitFor[currentChunk % batchSize]); + } + currentChunk++; + } + } + } + else if (workSizeDim == 3) + { + for (offset[0] = 0; offset[0] < m_GlobalWorkSize[0]; offset[0] += chunksDim[0]) + { + for (offset[1] = 0; offset[1] < m_GlobalWorkSize[1]; offset[1] += chunksDim[1]) + { + for (offset[2] = 0; offset[2] < m_GlobalWorkSize[2]; offset[2] += chunksDim[2]) + { + if (currentChunk % batchSize == 0 && currentChunk != 0) + { + clWaitForEvents(batchSize, &waitFor[0]); + std::this_thread::sleep_for(std::chrono::milliseconds(waitTimems)); + clErr |= clEnqueueNDRangeKernel(this->m_CommandQue, kernel, workSizeDim, + offset, chunksDim, m_LocalWorkSize, 0, nullptr, &waitFor[0]); + } + else + { + clErr |= clEnqueueNDRangeKernel(this->m_CommandQue, kernel, workSizeDim, + offset, chunksDim, m_LocalWorkSize, 0, nullptr, &waitFor[currentChunk % batchSize]); + } + currentChunk++; + } + } + } + } + CHECK_OCL_ERR(clErr); + + return (clErr == CL_SUCCESS); +} + bool mitk::OclFilter::Initialize() { us::ServiceReference ref = GetModuleContext()->GetServiceReference(); OclResourceService* resources = GetModuleContext()->GetService(ref); m_CommandQue = resources->GetCommandQueue(); cl_int clErr = 0; m_Initialized = CHECK_OCL_ERR(clErr); if ( m_ClFiles.empty()) { MITK_ERROR<<"No OpenCL Source FILE specified"; return false; } if (m_ClProgram == nullptr) { try { this->m_ClProgram = resources->GetProgram( this->m_FilterID ); } catch(const mitk::Exception& e) { - MITK_INFO << "Program not stored in resource manager, compiling."; + MITK_INFO << "Program not stored in resource manager, compiling. " << e; this->CompileSource(); } } return m_Initialized; } void mitk::OclFilter::LoadSourceFiles(CStringList &sourceCode, ClSizeList &sourceCodeSize) { for( CStringList::iterator it = m_ClFiles.begin(); it != m_ClFiles.end(); ++it ) { MITK_DEBUG << "Load file :" << *it; us::ModuleResource mdr = GetModule()->GetResource(*it); if( !mdr.IsValid() ) MITK_WARN << "Could not load resource: " << mdr.GetName() << " is invalid!"; us::ModuleResourceStream rss(mdr); // read resource file to a string std::istreambuf_iterator eos; std::string source(std::istreambuf_iterator(rss), eos); // add preambel and build up string to compile std::string src(m_Preambel); src.append("\n"); src.append(source); // allocate new char buffer char* tmp = new char[src.size() + 1]; strcpy(tmp,src.c_str()); // add source to list sourceCode.push_back((const char*)tmp); sourceCodeSize.push_back(src.size()); } } void mitk::OclFilter::CompileSource() { // helper variable int clErr = 0; CStringList sourceCode; ClSizeList sourceCodeSize; if (m_ClFiles.empty()) { MITK_ERROR("ocl.filter") << "No shader source file was set"; return; } //get a valid opencl context us::ServiceReference ref = GetModuleContext()->GetServiceReference(); OclResourceService* resources = GetModuleContext()->GetService(ref); cl_context gpuContext = resources->GetContext(); // load the program source from file LoadSourceFiles(sourceCode, sourceCodeSize); if ( !sourceCode.empty() ) { // create program from all files in the file list m_ClProgram = clCreateProgramWithSource(gpuContext, sourceCode.size(), &sourceCode[0], &sourceCodeSize[0], &clErr); CHECK_OCL_ERR(clErr); // build the source code MITK_DEBUG << "Building Program Source"; std::string compilerOptions = ""; compilerOptions.append(m_ClCompilerFlags); MITK_DEBUG("ocl.filter") << "cl compiler flags: " << compilerOptions.c_str(); clErr = clBuildProgram(m_ClProgram, 0, nullptr, compilerOptions.c_str(), nullptr, nullptr); CHECK_OCL_ERR(clErr); // if OpenCL Source build failed if (clErr != CL_SUCCESS) { MITK_ERROR("ocl.filter") << "Failed to build source"; oclLogBuildInfo(m_ClProgram, resources->GetCurrentDevice() ); oclLogBinary(m_ClProgram, resources->GetCurrentDevice() ); m_Initialized = false; } // store the succesfully build program into the program storage provided by the resource service resources->InsertProgram(m_ClProgram, m_FilterID, true); // free the char buffers with the source code for( CStringList::iterator it = sourceCode.begin(); it != sourceCode.end(); ++it ) { delete[] *it; } } else { MITK_ERROR("ocl.filter") << "Could not load from source"; m_Initialized = false; } } void mitk::OclFilter::SetWorkingSize(unsigned int locx, unsigned int dimx, unsigned int locy, unsigned int dimy, unsigned int locz, unsigned int dimz) { // set the local work size this->m_LocalWorkSize[0] = locx; this->m_LocalWorkSize[1] = locy; this->m_LocalWorkSize[2] = locz; this->m_GlobalWorkSize[0] = dimx; this->m_GlobalWorkSize[1] = dimy; this->m_GlobalWorkSize[2] = dimz; // estimate the global work size this->m_GlobalWorkSize[0] = iDivUp( dimx, this->m_LocalWorkSize[0]) * this->m_LocalWorkSize[0]; if ( dimy > 1) this->m_GlobalWorkSize[1] = iDivUp( dimy, this->m_LocalWorkSize[1]) * this->m_LocalWorkSize[1]; if( dimz > 1 ) this->m_GlobalWorkSize[2] = iDivUp( dimz, this->m_LocalWorkSize[2]) * this->m_LocalWorkSize[2]; } void mitk::OclFilter::SetSourcePreambel(const char* preambel) { this->m_Preambel = preambel; } void mitk::OclFilter::AddSourceFile(const char* filename) { m_ClFiles.push_back(filename); } void mitk::OclFilter::SetCompilerFlags(const char* flags) { m_ClCompilerFlags = flags; } bool mitk::OclFilter::IsInitialized() { return m_Initialized; } + +long mitk::OclFilter::GetDeviceMemory() +{ + OclResourceService* resources = GetModuleContext()->GetService(GetModuleContext()->GetServiceReference()); + auto device = resources->GetCurrentDevice(); + return oclGetGlobalMemSize(device); +} \ No newline at end of file diff --git a/Modules/OpenCL/mitkOclFilter.h b/Modules/OpenCL/mitkOclFilter.h index e4b1bb67fb..89f557bd07 100644 --- a/Modules/OpenCL/mitkOclFilter.h +++ b/Modules/OpenCL/mitkOclFilter.h @@ -1,149 +1,162 @@ /*=================================================================== 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 __mitkOclFilter_h #define __mitkOclFilter_h #include "mitkOclUtils.h" #include "mitkCommon.h" #include #include #include namespace mitk { /** @class OclFilter @brief Superclass for all OpenCL based filter. This class takes care of loading and compiling the external GPU program code. */ class MITKOPENCL_EXPORT OclFilter { public: /** * @brief Add a source file from the resource files to the * OpenCL shader file list. Multiple files can be added to the list. * * @param name of the file in the resource system */ void AddSourceFile(const char* filename); /** * @brief Set specific compilerflags to compile the CL source. Default is set to nullptr; * example: "-cl-fast-relaxed-math -cl-mad-enable -cl-strict-aliasing" * * @param flags to the modulefolder that contains the gpuSource */ void SetCompilerFlags(const char* flags); /** * @brief Returns true if the initialization was successfull */ virtual bool IsInitialized(); + /** + * @brief Returns the amount of global memory of the used device in bytes + */ + virtual long GetDeviceMemory(); + /** @brief Destructor */ virtual ~OclFilter(); protected: typedef std::vector CStringList; typedef std::vector ClSizeList; /** @brief Constructor */ OclFilter(); /** @brief Constructor ( overloaded ) */ OclFilter(const char* filename); /** @brief String that contains the compiler flags */ const char* m_ClCompilerFlags; /** @brief The compiled OpenCL program */ cl_program m_ClProgram; /** @brief Command queue for the filter */ cl_command_queue m_CommandQue; /** @brief Unique ID of the filter, needs to be specified in the constructor of the derived class */ std::string m_FilterID; /*! @brief source preambel for e.g. #define commands to be inserted into the OpenCL source */ const char* m_Preambel; /** @brief List of sourcefiles that will be compiled for this filter.*/ CStringList m_ClFiles; /** @brief status of the filter */ bool m_Initialized; /** @brief The local work size fo the filter */ size_t m_LocalWorkSize[3]; /** @brief The global work size of the filter */ size_t m_GlobalWorkSize[3]; /** @brief Set the working size for the following OpenCL kernel call */ void SetWorkingSize(unsigned int locx, unsigned int dimx, unsigned int locy = 1, unsigned int dimy = 1, unsigned int locz = 1, unsigned int dimz = 1); /** @brief Execute the given kernel on the OpenCL Index-Space defined by the local and global work sizes */ bool ExecuteKernel( cl_kernel kernel, unsigned int workSizeDim ); + /** @brief Execute the given kernel on the OpenCL Index-Space defined by the local and global work sizes, but divide it into chunks of dimension chunksDim + */ + bool ExecuteKernelChunks( cl_kernel kernel, unsigned int workSizeDim, size_t* chunksDim ); + + /** @brief Execute the given kernel on the OpenCL Index-Space defined by the local and global work sizes, but divide it into chunks of dimension chunksDim and wait between + * batches of batchSize chunks a time of waitTimems milliseconds + */ + bool ExecuteKernelChunksInBatches(cl_kernel kernel, unsigned int workSizeDim, size_t* chunksDim, size_t batchSize, int waitTimems); /** * \brief Initialize all necessary parts of the filter * * The Initialize() method creates the command queue and the m_clProgram. * The program is either compiled from the given source or taken from the * OclResourceManager if the program was compiled already. */ bool Initialize(); /** * @brief Compile the program source * * @param preambel e.g. defines for the shader code */ void CompileSource(); /** * @brief Add some source code on the beginning of the loaded source * * In this way, some preprocessor flags for the CL compiler can at the beginning of the filter * @param preambel Source preambel for e.g. #define commands to be inserted into the OpenCL source */ void SetSourcePreambel(const char* preambel); /** * @brief Get the Module of the filter. Needs to be implemented by every subclass. * The filter will load the OpenCL sourcefiles from this module context. */ virtual us::Module* GetModule() = 0; /** * @brief Helper functions that load sourcefiles from the module context in the Initialize function. * @param SourceCodeList holds the sourcecode for every file as string, the SourceCodeSizeList holst the * size of every file in bytes. */ void LoadSourceFiles(CStringList &SourceCodeList, ClSizeList &SourceCodeSizeList); }; } #endif // __mitkOclFilter_h diff --git a/Modules/OpenCL/mitkOclImageToImageFilter.cpp b/Modules/OpenCL/mitkOclImageToImageFilter.cpp index f78d6f9def..10f88b06a4 100644 --- a/Modules/OpenCL/mitkOclImageToImageFilter.cpp +++ b/Modules/OpenCL/mitkOclImageToImageFilter.cpp @@ -1,193 +1,193 @@ /*=================================================================== 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 "mitkOclImageToImageFilter.h" #include "mitkOclImage.h" #include "mitkException.h" mitk::OclImageToImageFilter::OclImageToImageFilter() { m_Output = mitk::OclImage::New(); } mitk::OclImageToImageFilter::~OclImageToImageFilter() { } mitk::OclImage::Pointer mitk::OclImageToImageFilter::GetGPUOutput() { // initialize some variables m_Output->SetPixelType(m_Input->GetPixelType()); // create new image, for passing the essential information to the output m_Output->InitializeMITKImage(); const unsigned int dimension = m_Input->GetDimension(); unsigned int* dimensions = m_Input->GetDimensions(); m_Output->SetDimensions( dimensions ); m_Output->SetDimension( (unsigned short)dimension ); m_Output->GetMITKImage()->Initialize( this->GetOutputType(), dimension, dimensions); const mitk::SlicedGeometry3D::Pointer p_slg = m_Input->GetMITKImage()->GetSlicedGeometry(0); m_Output->GetMITKImage()->SetSpacing( p_slg->GetSpacing() ); m_Output->GetMITKImage()->SetGeometry( m_Input->GetMITKImage()->GetGeometry() ); return this->m_Output; } mitk::Image::Pointer mitk::OclImageToImageFilter::GetOutput() { if (m_Output->IsModified(GPU_DATA)) { void* pData = m_Output->TransferDataToCPU(m_CommandQue); const unsigned int dimension = m_Input->GetDimension(); unsigned int* dimensions = m_Input->GetDimensions(); const mitk::SlicedGeometry3D::Pointer p_slg = m_Input->GetMITKImage()->GetSlicedGeometry(); MITK_DEBUG << "Creating new MITK Image."; m_Output->GetMITKImage()->Initialize( this->GetOutputType(), dimension, dimensions); m_Output->GetMITKImage()->SetSpacing( p_slg->GetSpacing()); m_Output->GetMITKImage()->SetGeometry( m_Input->GetMITKImage()->GetGeometry() ); m_Output->GetMITKImage()->SetImportVolume( pData, 0, 0, mitk::Image::ReferenceMemory); } MITK_DEBUG << "Image Initialized."; return m_Output->GetMITKImage(); } mitk::PixelType mitk::OclImageToImageFilter::GetOutputType() { // get the current image format from the input image const cl_image_format* currentImFormat = this->m_Input->GetPixelType(); // return the value according to the current channel type switch( currentImFormat->image_channel_data_type ) { case CL_UNORM_INT8: return mitk::MakeScalarPixelType(); case CL_UNSIGNED_INT8: return mitk::MakeScalarPixelType(); case CL_UNORM_INT16: return mitk::MakeScalarPixelType(); default: return mitk::MakeScalarPixelType(); } } int mitk::OclImageToImageFilter::GetBytesPerElem() { return (this->m_CurrentType + 1); } bool mitk::OclImageToImageFilter::InitExec(cl_kernel ckKernel) { cl_int clErr = 0; if( m_Input.IsNull() ) mitkThrow() << "Input image is null."; // get image size once const unsigned int uiImageWidth = m_Input->GetDimension(0); const unsigned int uiImageHeight = m_Input->GetDimension(1); const unsigned int uiImageDepth = m_Input->GetDimension(2); // compute work sizes this->SetWorkingSize( 8, uiImageWidth, 8, uiImageHeight , 8, uiImageDepth ); cl_mem clBuffIn = m_Input->GetGPUImage(this->m_CommandQue); cl_mem clBuffOut = m_Output->GetGPUBuffer(); if (!clBuffIn) { if ( m_Input->TransferDataToGPU(m_CommandQue) != CL_SUCCESS ) { mitkThrow()<< "Could not create / initialize gpu image."; } clBuffIn = m_Input->GetGPUImage(m_CommandQue); } // output image not initialized if (!clBuffOut) { //TODO bpp, or SetImageWidth/Height/... MITK_DEBUG << "Create GPU Image call " << uiImageWidth<< "x"<CreateGPUImage(uiImageWidth, uiImageHeight, uiImageDepth, this->m_CurrentType + 1); } clErr = 0; clErr = clSetKernelArg(ckKernel, 0, sizeof(cl_mem), &clBuffIn); clErr |= clSetKernelArg(ckKernel, 1, sizeof(cl_mem), &clBuffOut); CHECK_OCL_ERR( clErr ); if( clErr != CL_SUCCESS ) mitkThrow() << "OpenCL Part initialization failed with " << GetOclErrorAsString(clErr); return( clErr == CL_SUCCESS ); } bool mitk::OclImageToImageFilter::InitExec(cl_kernel ckKernel, unsigned int* dimensions) { cl_int clErr = 0; if( m_Input.IsNull() ) mitkThrow() << "Input image is null."; // get image size once const unsigned int uiImageWidth = dimensions[0]; const unsigned int uiImageHeight = dimensions[1]; - const unsigned int uiImageDepth = dimensions[2]; + const unsigned int uiImageDepth = dimensions[2]+1; // compute work sizes this->SetWorkingSize( 8, uiImageWidth, 8, uiImageHeight , 8, uiImageDepth ); cl_mem clBuffIn = m_Input->GetGPUImage(this->m_CommandQue); cl_mem clBuffOut = m_Output->GetGPUBuffer(); if (!clBuffIn) { if ( m_Input->TransferDataToGPU(m_CommandQue) != CL_SUCCESS ) { mitkThrow()<< "Could not create / initialize gpu image."; } clBuffIn = m_Input->GetGPUImage(m_CommandQue); } // output image not initialized //TODO bpp, or SetImageWidth/Height/... MITK_INFO << "Create GPU Image call " << uiImageWidth<< "x"<CreateGPUImage(uiImageWidth, uiImageHeight, uiImageDepth, this->m_CurrentType + 1); clErr = 0; clErr = clSetKernelArg(ckKernel, 0, sizeof(cl_mem), &clBuffIn); clErr |= clSetKernelArg(ckKernel, 1, sizeof(cl_mem), &clBuffOut); CHECK_OCL_ERR( clErr ); if( clErr != CL_SUCCESS ) mitkThrow() << "OpenCL Part initialization failed with " << GetOclErrorAsString(clErr); return( clErr == CL_SUCCESS ); } \ No newline at end of file diff --git a/Modules/OpenCL/mitkOclUtils.cpp b/Modules/OpenCL/mitkOclUtils.cpp index d743b3d494..79970ce3af 100644 --- a/Modules/OpenCL/mitkOclUtils.cpp +++ b/Modules/OpenCL/mitkOclUtils.cpp @@ -1,572 +1,583 @@ /*=================================================================== 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 "mitkOclUtils.h" #include "mitkLogMacros.h" #include #include unsigned int iDivUp(unsigned int dividend, unsigned int divisor){ return (dividend % divisor == 0) ? (dividend / divisor) : (dividend / divisor + 1); } cl_int oclGetPlatformID(cl_platform_id* selectedPlatform) { cl_uint num_platforms = 0; cl_platform_id* clPlatformIDs; cl_int ciErrNum = 0; ciErrNum = clGetPlatformIDs( 0, nullptr, &num_platforms); if ( ciErrNum != CL_SUCCESS) { MITK_ERROR<<" Error " << ciErrNum << " in clGetPlatformIDs() \n"; throw std::bad_exception(); } else { clPlatformIDs = new cl_platform_id[num_platforms]; ciErrNum = clGetPlatformIDs( num_platforms, clPlatformIDs, nullptr); if(ciErrNum == CL_SUCCESS) { *selectedPlatform = clPlatformIDs[0]; } } return CL_SUCCESS; } void oclPrintMemObjectInfo(cl_mem memobj) { cl_int clErr = 0; MITK_INFO << "Examining cl_mem object: " << memobj << "\n------------------\n"; // CL_MEM_TYPE cl_mem_object_type objtype; clErr = clGetMemObjectInfo( memobj, CL_MEM_TYPE, sizeof(cl_mem_object_type),&objtype, nullptr); CHECK_OCL_ERR( clErr ); switch(objtype) { case CL_MEM_OBJECT_BUFFER: MITK_INFO << "CL_MEM_TYPE \t" << "BUFFER_OBJ" << "\n"; break; case CL_MEM_OBJECT_IMAGE2D: MITK_INFO << "CL_MEM_TYPE \t" << "2D IMAGE" << "\n"; break; case CL_MEM_OBJECT_IMAGE3D: MITK_INFO << "CL_MEM_TYPE \t" << "3D IMAGE" << "\n"; break; default: MITK_INFO << "CL_MEM_TYPE \t" << "[could not resolve]" << "\n"; break; } // CL_MEM_FLAGS cl_mem_flags flags; clErr = clGetMemObjectInfo( memobj, CL_MEM_FLAGS, sizeof(cl_mem_flags),&flags, nullptr); CHECK_OCL_ERR( clErr ); switch(flags) { case CL_MEM_READ_ONLY: MITK_INFO << "CL_MEM_FLAGS \t" << "CL_MEM_READ_ONLY" << "\n"; break; case CL_MEM_WRITE_ONLY: MITK_INFO << "CL_MEM_FLAGS \t" << "CL_MEM_WRITE_ONLY" << "\n"; break; case CL_MEM_READ_WRITE: MITK_INFO << "CL_MEM_FLAGS \t" << "CL_MEM_READ_WRITE" << "\n"; break; default: MITK_INFO << "CL_MEM_FLAGS \t" << "not resolved, " << flags << "\n"; break; } // get CL_MEM_SIZE size_t memsize; clErr = clGetMemObjectInfo( memobj, CL_MEM_SIZE, sizeof(memsize),&memsize, nullptr); CHECK_OCL_ERR( clErr ); MITK_INFO << "CL_MEM_SIZE \t" << memsize << "\n"; // get CL_MEM_HOST_PTR float *hostptr; clErr = clGetMemObjectInfo( memobj, CL_MEM_HOST_PTR, sizeof(void*), (void*) &hostptr, nullptr); CHECK_OCL_ERR( clErr ); MITK_INFO << "CL_MEM_HOST_PTR \t" << hostptr << "\n"; // get CL_CONTEXT cl_context gpuctxt; clErr = clGetMemObjectInfo( memobj, CL_MEM_CONTEXT, sizeof(cl_context), &gpuctxt, nullptr); CHECK_OCL_ERR( clErr ); MITK_INFO << "CL_CONTEXT \t\t" << gpuctxt << "\n"; // get CL_MEM_REFERENCE_COUNT cl_uint refs; clErr = clGetMemObjectInfo( memobj, CL_MEM_REFERENCE_COUNT, sizeof(cl_uint), &refs, nullptr); CHECK_OCL_ERR(clErr); MITK_INFO << "CL_REF_COUNT \t" << refs << "\n"; MITK_INFO << "================== \n" << std::endl; } void oclPrintDeviceInfo(cl_device_id device) { char device_string[1024]; clGetDeviceInfo(device, CL_DEVICE_NAME, sizeof(device_string), &device_string, nullptr); MITK_INFO("ocl.log")<< " Device : " << device_string; // CL_DEVICE_INFO cl_device_type type; clGetDeviceInfo(device, CL_DEVICE_TYPE, sizeof(type), &type, nullptr); if( type & CL_DEVICE_TYPE_CPU ) MITK_INFO("ocl.log")<<" CL_DEVICE_TYPE: CL_DEVICE_TYPE_CPU"; if( type & CL_DEVICE_TYPE_GPU ) MITK_INFO("ocl.log")<<" CL_DEVICE_TYPE: CL_DEVICE_TYPE_GPU"; if( type & CL_DEVICE_TYPE_ACCELERATOR ) MITK_INFO("ocl.log")<<" CL_DEVICE_TYPE: CL_DEVICE_TYPE_ACCELERATOR"; if( type & CL_DEVICE_TYPE_DEFAULT ) MITK_INFO("ocl.log")<<" CL_DEVICE_TYPE: CL_DEVICE_TYPE_DEFAULT"; // CL_DEVICE_MAX_COMPUTE_UNITS cl_uint compute_units; clGetDeviceInfo(device, CL_DEVICE_MAX_COMPUTE_UNITS, sizeof(compute_units), &compute_units, nullptr); MITK_INFO("ocl.log")<<" CL_DEVICE_MAX_COMPUTE_UNITS:" << compute_units; // CL_DEVICE_MAX_WORK_GROUP_SIZE size_t workitem_size[3]; clGetDeviceInfo(device, CL_DEVICE_MAX_WORK_ITEM_SIZES, sizeof(workitem_size), &workitem_size, nullptr); MITK_INFO("ocl.log")<<" CL_DEVICE_MAX_WORK_ITEM_SIZES:\t"<< workitem_size[0]<< workitem_size[1]<< workitem_size[2]; // CL_DEVICE_MAX_WORK_GROUP_SIZE size_t workgroup_size; clGetDeviceInfo(device, CL_DEVICE_MAX_WORK_GROUP_SIZE, sizeof(workgroup_size), &workgroup_size, nullptr); MITK_INFO("ocl.log")<<" CL_DEVICE_MAX_WORK_GROUP_SIZE:" << workgroup_size; // CL_DEVICE_MAX_CLOCK_FREQUENCY cl_uint clock_frequency; clGetDeviceInfo(device, CL_DEVICE_MAX_CLOCK_FREQUENCY, sizeof(clock_frequency), &clock_frequency, nullptr); MITK_INFO("ocl.log")<<" CL_DEVICE_MAX_CLOCK_FREQUENCY:"<< clock_frequency / 1000; // CL_DEVICE_IMAGE_SUPPORT cl_bool image_support; clGetDeviceInfo(device, CL_DEVICE_IMAGE_SUPPORT, sizeof(image_support), &image_support, nullptr); MITK_INFO("ocl.log")<<" CL_DEVICE_IMAGE_SUPPORT:\t" << image_support; // CL_DEVICE_GLOBAL_MEM_SIZE cl_ulong mem_size; clGetDeviceInfo(device, CL_DEVICE_GLOBAL_MEM_SIZE, sizeof(mem_size), &mem_size, nullptr); MITK_INFO("ocl.log")<<" CL_DEVICE_GLOBAL_MEM_SIZE:\t\t"<<(unsigned int)(mem_size / (1024 * 1024))<<"Mbytes"; // CL_DEVICE_LOCAL_MEM_SIZE clGetDeviceInfo(device, CL_DEVICE_LOCAL_MEM_SIZE, sizeof(mem_size), &mem_size, nullptr); MITK_INFO("ocl.log")<<" CL_DEVICE_LOCAL_MEM_SIZE:\t\t"<< (unsigned int)(mem_size / (1024)) <<"KByte\n"; + // CL_DEVICE_MAX_CONSTANT_BUFFER_SIZE + clGetDeviceInfo(device, CL_DEVICE_MAX_CONSTANT_BUFFER_SIZE, sizeof(mem_size), &mem_size, nullptr); + MITK_INFO("ocl.log") << " CL_DEVICE_MAX_CONSTANT_BUFFER_SIZE:\t\t" << (unsigned int)(mem_size / (1024)) << "KByte"; + //check for image support properties clGetDeviceInfo(device, CL_DEVICE_IMAGE2D_MAX_WIDTH, sizeof(workgroup_size), &workgroup_size, nullptr); MITK_INFO("ocl.log")<<" CL_DEVICE_IMAGE2D_MAX_WIDTH:\t" << workgroup_size; clGetDeviceInfo(device, CL_DEVICE_IMAGE2D_MAX_HEIGHT, sizeof(workgroup_size), &workgroup_size, nullptr); MITK_INFO("ocl.log")<<" CL_DEVICE_IMAGE2D_MAX_HEIGHT:\t" << workgroup_size; clGetDeviceInfo(device, CL_DEVICE_IMAGE3D_MAX_WIDTH, sizeof(workgroup_size), &workgroup_size, nullptr); MITK_INFO("ocl.log")<<" CL_DEVICE_IMAGE3D_MAX_WIDTH:\t" << workgroup_size; clGetDeviceInfo(device, CL_DEVICE_IMAGE3D_MAX_HEIGHT, sizeof(workgroup_size), &workgroup_size, nullptr); MITK_INFO("ocl.log")<<" CL_DEVICE_IMAGE3D_MAX_HEIGHT:\t" << workgroup_size; clGetDeviceInfo(device, CL_DEVICE_IMAGE3D_MAX_DEPTH, sizeof(workgroup_size), &workgroup_size, nullptr); MITK_INFO("ocl.log")<<" CL_DEVICE_IMAGE3D_MAX_DEPTH:\t" << workgroup_size; // CL_DEVICE_QUEUE_PROPERTIES cl_command_queue_properties queue_properties; clGetDeviceInfo(device, CL_DEVICE_QUEUE_PROPERTIES, sizeof(queue_properties), &queue_properties, nullptr); if( queue_properties & CL_QUEUE_OUT_OF_ORDER_EXEC_MODE_ENABLE ) MITK_INFO("ocl.log")<<" CL_DEVICE_QUEUE_PROPERTIES:\t\t"<< "CL_QUEUE_OUT_OF_ORDER_EXEC_MODE_ENABLE"; if( queue_properties & CL_QUEUE_PROFILING_ENABLE ) MITK_INFO("ocl.log")<<" CL_DEVICE_QUEUE_PROPERTIES:\t\t"<< "CL_QUEUE_PROFILING_ENABLE"; } +cl_ulong oclGetGlobalMemSize(cl_device_id device) +{ + cl_ulong mem_size; + clGetDeviceInfo(device, CL_DEVICE_GLOBAL_MEM_SIZE, sizeof(mem_size), &mem_size, nullptr); + return mem_size; +} + std::string GetOclErrorAsString( int _clErr ) { std::string returnString("unkown error number: "+std::to_string(_clErr)+" \n"); switch(_clErr) { case CL_SUCCESS: returnString = "CL_SUCCESS\n"; break; case CL_DEVICE_NOT_FOUND: returnString = "CL_DEVICE_NOT_FOUND\n"; break; case CL_DEVICE_NOT_AVAILABLE: returnString = "CL_DEVICE_NOT_AVAILABLE\n"; break; /*case CL_DEVICE_COMPILER_NOT_AVAILABLE: returnString = "CL_DEVICE_COMPILER_NOT_AVAILABLE\n"; break; */ case CL_MEM_OBJECT_ALLOCATION_FAILURE : returnString = "CL_MEM_OBJECT_ALLOCATION_FAILURE\n"; break; case CL_OUT_OF_RESOURCES: returnString = "CL_OUT_OF_RESOURCES\n"; break; case CL_OUT_OF_HOST_MEMORY: returnString = "CL_OUT_OF_HOST_MEMORY\n"; break; case CL_PROFILING_INFO_NOT_AVAILABLE: returnString = "CL_PROFILING_INFO_NOT_AVAILABLE\n"; break; case CL_MEM_COPY_OVERLAP: returnString = "CL_MEM_COPY_OVERLAP\n"; break; case CL_IMAGE_FORMAT_MISMATCH: returnString = "CL_IMAGE_FORMAT_MISMATCH\n"; break; case CL_IMAGE_FORMAT_NOT_SUPPORTED: returnString = "CL_IMAGE_FORMAT_NOT_SUPPORTED\n"; break; case CL_BUILD_PROGRAM_FAILURE: returnString = "CL_BUILD_PROGRAM_FAILURE\n"; break; case CL_MAP_FAILURE: returnString = "CL_MAP_FAILURE\n"; break; case CL_INVALID_VALUE: returnString = "CL_INVALID_VALUE\n"; break; case CL_INVALID_DEVICE_TYPE: returnString = "CL_INVALID_DEVICE_TYPE\n"; break; case CL_INVALID_PLATFORM: returnString = "CL_INVALID_PLATFORM\n"; break; case CL_INVALID_DEVICE: returnString = "CL_INVALID_DEVICE\n"; break; case CL_INVALID_CONTEXT : returnString = "CL_INVALID_CONTEXT\n"; break; case CL_INVALID_QUEUE_PROPERTIES: returnString = "CL_INVALID_QUEUE_PROPERTIES\n"; break; case CL_INVALID_COMMAND_QUEUE: returnString = "CL_INVALID_COMMAND_QUEUE\n"; break; case CL_INVALID_HOST_PTR: returnString = "CL_INVALID_HOST_PTR\n"; break; case CL_INVALID_MEM_OBJECT: returnString = "CL_INVALID_MEM_OBJECT\n"; break; case CL_INVALID_IMAGE_FORMAT_DESCRIPTOR: returnString = "CL_INVALID_IMAGE_FORMAT_DESCRIPTOR\n"; break; case CL_INVALID_IMAGE_SIZE: returnString = "CL_INVALID_IMAGE_SIZE\n"; break; case CL_INVALID_SAMPLER : returnString = "CL_INVALID_SAMPLER\n"; break; case CL_INVALID_BINARY: returnString = "CL_INVALID_BINARY\n"; break; case CL_INVALID_BUILD_OPTIONS: returnString = "CL_INVALID_BUILD_OPTIONS\n"; break; case CL_INVALID_PROGRAM: returnString = "CL_INVALID_PROGRAM\n"; break; case CL_INVALID_PROGRAM_EXECUTABLE: returnString = "CL_INVALID_PROGRAM_EXECUTABLE\n"; break; case CL_INVALID_KERNEL_NAME: returnString = "CL_INVALID_KERNEL_NAME\n"; break; case CL_INVALID_KERNEL_DEFINITION: returnString = "CL_INVALID_KERNEL_DEFINITION\n"; break; case CL_INVALID_KERNEL : returnString = "CL_INVALID_KERNEL\n"; break; case CL_INVALID_ARG_INDEX : returnString = "CL_INVALID_ARG_INDEX\n"; break; case CL_INVALID_ARG_VALUE : returnString = "CL_INVALID_ARG_VALUE\n"; break; case CL_INVALID_ARG_SIZE : returnString = "CL_INVALID_ARG_SIZE\n"; break; case CL_INVALID_KERNEL_ARGS : returnString = "CL_INVALID_KERNEL_ARGS\n"; break; case CL_INVALID_WORK_DIMENSION: returnString = "CL_INVALID_WORK_DIMENSION\n"; break; case CL_INVALID_WORK_GROUP_SIZE: returnString = "CL_INVALID_WORK_GROUP_SIZE\n"; break; case CL_INVALID_WORK_ITEM_SIZE: returnString = "CL_INVALID_WORK_ITEM_SIZE\n"; break; case CL_INVALID_GLOBAL_OFFSET: returnString = "CL_INVALID_GLOBAL_OFFSET\n"; break; case CL_INVALID_EVENT_WAIT_LIST: returnString = "CL_INVALID_EVENT_WAIT_LIST\n"; break; case CL_INVALID_EVENT: returnString = "CL_INVALID_EVENT\n"; break; case CL_INVALID_OPERATION: returnString = "CL_INVALID_OPERATION\n"; break; case CL_INVALID_GL_OBJECT: returnString = "CL_INVALID_GL_OBJECT\n"; break; case CL_INVALID_BUFFER_SIZE : returnString = "CL_INVALID_BUFFER_SIZE\n"; break; case CL_INVALID_MIP_LEVEL : returnString = "CL_INVALID_MIP_LEVEL\n"; break; default: break; } return returnString; } void GetOclError(int _clErr) { if(_clErr == CL_SUCCESS) MITK_WARN << "Called GetOclErr() with no error value: [CL_SUCCESS]"; else MITK_ERROR << GetOclErrorAsString(_clErr); } bool oclCheckError(int _err, const char* filepath, int lineno) { if (_err) { MITK_ERROR<< "OpenCL Error at " << filepath <<":"<< lineno; GetOclError(_err); return 0; } return 1; } void GetSupportedImageFormats(cl_context _context, cl_mem_object_type _type) { const unsigned int entries = 500; cl_image_format* formats = new cl_image_format[entries]; cl_uint _written = 0; // OpenCL constant to catch error IDs cl_int ciErr1; // Get list of supported image formats for READ_ONLY access ciErr1 = clGetSupportedImageFormats( _context, CL_MEM_READ_ONLY, _type, entries, formats, &_written); CHECK_OCL_ERR(ciErr1); MITK_INFO << "Supported Image Formats, Image: CL_MEM_READ_ONLY \n"; for (unsigned int i=0; i<_written; i++) { MITK_INFO<< "ChannelType: " << GetImageTypeAsString(formats[i].image_channel_data_type) << "| ChannelOrder: "<< GetImageTypeAsString(formats[i].image_channel_order) <<"\n"; } _written = 0; // Get list of supported image formats for READ_WRITE access ciErr1 = clGetSupportedImageFormats( _context, CL_MEM_READ_WRITE, _type, entries, formats, &_written); CHECK_OCL_ERR(ciErr1); MITK_INFO << "Supported Image Formats, Image: CL_MEM_READ_WRITE (found: " << _written <<") \n"; for (unsigned int i=0; i<_written; i++) { MITK_INFO<< "ChannelType: " << GetImageTypeAsString(formats[i].image_channel_data_type) << "| ChannelOrder: "<< GetImageTypeAsString(formats[i].image_channel_order) <<"\n"; } _written = 0; // Get list of supported image formats for WRITE_ONLY access ciErr1 = clGetSupportedImageFormats( _context, CL_MEM_WRITE_ONLY, _type, entries, formats, &_written); CHECK_OCL_ERR(ciErr1); MITK_INFO << "Supported Image Formats, Image: CL_MEM_WRITE_ONLY (found: " << _written <<") \n"; for (unsigned int i=0; i<_written; i++) { MITK_INFO<< "ChannelType: " << GetImageTypeAsString(formats[i].image_channel_data_type) << "| ChannelOrder: "<< GetImageTypeAsString(formats[i].image_channel_order) <<"\n"; } } std::string GetImageTypeAsString( const unsigned int _in) { switch(_in) { case CL_R: return "CL_R "; break; case CL_A: return "CL_A "; break; case CL_RG: return "CL_RG "; break; case CL_RA: return "CL_RA "; break; case CL_RGB: return "CL_RGB "; break; case CL_RGBA: return "CL_RGBA "; break; case CL_BGRA: return "CL_BGRA "; break; case CL_ARGB: return "CL_ARGB "; break; case CL_INTENSITY: return "CL_INTENSITY "; break; case CL_LUMINANCE: return "CL_LUMINANCE "; break; case CL_SNORM_INT8: return "CL_SNORM_INT8 "; break; case CL_SNORM_INT16: return "CL_SNORM_INT16 "; break; case CL_UNORM_INT8: return "CL_UNORM_INT8 "; break; case CL_UNORM_INT16: return "CL_UNORM_INT16 "; break; case CL_UNORM_SHORT_565: return "CL_UNORM_SHORT_565 "; break; case CL_UNORM_SHORT_555: return "CL_UNORM_SHORT_555 "; break; case CL_UNORM_INT_101010: return "CL_UNORM_INT_101010 "; break; case CL_SIGNED_INT8: return "CL_SIGNED_INT8 "; break; case CL_SIGNED_INT16: return "CL_SIGNED_INT16 "; break; case CL_SIGNED_INT32: return "CL_SIGNED_INT32 "; break; case CL_UNSIGNED_INT8: return "CL_UNSIGNED_INT8 "; break; case CL_UNSIGNED_INT16: return "CL_UNSIGNED_INT16 "; break; case CL_UNSIGNED_INT32: return "CL_UNSIGNED_INT32 "; break; case CL_HALF_FLOAT: return "CL_HALF_FLOAT "; break; case CL_FLOAT: return "CL_FLOAT "; break; default: return "--"; break; } } void oclLogBinary(cl_program clProg, cl_device_id clDev) { // Grab the number of devices associated with the program cl_uint num_devices; clGetProgramInfo(clProg, CL_PROGRAM_NUM_DEVICES, sizeof(cl_uint), &num_devices, nullptr); // Grab the device ids cl_device_id* devices = (cl_device_id*) malloc(num_devices * sizeof(cl_device_id)); clGetProgramInfo(clProg, CL_PROGRAM_DEVICES, num_devices * sizeof(cl_device_id), devices, 0); // Grab the sizes of the binaries size_t* binary_sizes = (size_t*)malloc(num_devices * sizeof(size_t)); clGetProgramInfo(clProg, CL_PROGRAM_BINARY_SIZES, num_devices * sizeof(size_t), binary_sizes, nullptr); // Now get the binaries char** ptx_code = (char**)malloc(num_devices * sizeof(char*)); for( unsigned int i=0; i #include #define CHECK_OCL_ERR(_er) oclCheckError(_er, __FILE__, __LINE__); /** @brief Method to estimate an integer quotient C from given dividend and divisor higher or equal to the corresponding floating quotient If the divisor is a factor of the dividend, the dividend/divisor is an integer value and is returned. If not, the nearest higher integer is returned. So it holds for the return value C that C * divisor is equal or greater then the dividend. In OpenCL context useful for estimating the local/global working dimension of a NDRange so that all image data is covered by the parallelisation scheme. */ MITKOPENCL_EXPORT unsigned int iDivUp(unsigned int dividend, unsigned int divisor); /** @brief Returns the name of an OpenCL Error as a string Most of the OpenCL Methods ( cl ) return an integer error code. This method translates the error value given as parameter to the corresponding error name. For example the value -30 will be translated to CL_INVALID_VALUE */ MITKOPENCL_EXPORT std::string GetOclErrorAsString( int _clErr ); /** @brief Checks whether the given value corresponds to an OpenCL Error value and prints this message out as MITK_ERROR if yes */ MITKOPENCL_EXPORT void GetOclError(int _clErr); /** @brief Returns a platform ID of an OpenCL-capable GPU, or throws an exception */ MITKOPENCL_EXPORT cl_int oclGetPlatformID(cl_platform_id* selectedPlatform); /*! \brief Prints out the essential support information about current device */ MITKOPENCL_EXPORT void oclPrintDeviceInfo(cl_device_id); +/*! \brief Returns the Global memory size of the current device */ +MITKOPENCL_EXPORT cl_ulong oclGetGlobalMemSize(cl_device_id device); + /*! @brief Prints the available memory info about the given object to std::cout */ MITKOPENCL_EXPORT void oclPrintMemObjectInfo( cl_mem memobj); /*! \brief Checks the given code for errors and produces a std::cout output if the _err does not equal CL_SUCCESS. The output includes also the filename and the line number of the method call. */ MITKOPENCL_EXPORT bool oclCheckError(int _err, const char*, int); /*! \brief Logs the GPU Program binary code @param clProg: the OpenCL Program to log @param clDev: the OpenCL-capable device the program was tried to be compiled for */ MITKOPENCL_EXPORT void oclLogBinary(cl_program clProg, cl_device_id clDev); /*! \brief Shows the OpenCL-Program build info, called if clBuildProgram != CL_SUCCES @param clProg: the OpenCL Program to log @param clDev: the OpenCL-capable device the program was tried to be compiled for */ MITKOPENCL_EXPORT void oclLogBuildInfo(cl_program clProg, cl_device_id clDev); /** \brief Print out all supported image formats for given image type @param _type the image type ( CL_MEM_OBJECT_2D or CL_MEM_OBJECT_3D ) @param _context the OpenCL context to be examined */ MITKOPENCL_EXPORT void GetSupportedImageFormats(cl_context _context, cl_mem_object_type _type); /** @brief Translates the internal image type identifier to a human readable description string */ MITKOPENCL_EXPORT std::string GetImageTypeAsString( const unsigned int _in); #endif //mitkOclUtils_h diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/OCL/mitkPhotoacousticBModeFilter.cpp b/Modules/PhotoacousticsAlgorithms/Algorithms/OCL/mitkPhotoacousticBModeFilter.cpp deleted file mode 100644 index 891839b80a..0000000000 --- a/Modules/PhotoacousticsAlgorithms/Algorithms/OCL/mitkPhotoacousticBModeFilter.cpp +++ /dev/null @@ -1,103 +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. - -===================================================================*/ - -#include "mitkPhotoacousticBModeFilter.h" -#include "usServiceReference.h" - -mitk::PhotoacousticBModeFilter::PhotoacousticBModeFilter() - : m_PixelCalculation(NULL) -{ - this->AddSourceFile("BModeAbs.cl"); - this->AddSourceFile("BModeAbsLog.cl"); - - this->m_FilterID = "PixelCalculation"; -} - -mitk::PhotoacousticBModeFilter::~PhotoacousticBModeFilter() -{ - if (this->m_PixelCalculation) - { - clReleaseKernel(m_PixelCalculation); - } -} - -void mitk::PhotoacousticBModeFilter::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::PhotoacousticBModeFilter::Execute() -{ - try - { - this->InitExec(this->m_PixelCalculation); - } - catch (const mitk::Exception& e) - { - MITK_ERROR << "Catched exception while initializing filter: " << e.what(); - return; - } - - // execute the filter on a 3D NDRange - this->ExecuteKernel(m_PixelCalculation, 3); - - // signalize the GPU-side data changed - m_Output->Modified(GPU_DATA); -} - -us::Module *mitk::PhotoacousticBModeFilter::GetModule() -{ - return us::GetModuleContext()->GetModule(); -} - -bool mitk::PhotoacousticBModeFilter::Initialize() -{ - bool buildErr = true; - cl_int clErr = 0; - - if (OclFilter::Initialize()) - { - if(m_UseLogFilter) - this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckBmodeAbsLog", &clErr); - else - this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckBmodeAbs", &clErr); - buildErr |= CHECK_OCL_ERR(clErr); - } - return (OclFilter::IsInitialized() && buildErr); -} - -void mitk::PhotoacousticBModeFilter::SetInput(mitk::Image::Pointer image) -{ - if (image->GetDimension() != 3) - { - mitkThrowException(mitk::Exception) << "Input for " << this->GetNameOfClass() << - " is not 3D. The filter only supports 3D. Please change your input."; - } - OclImageToImageFilter::SetInput(image); -} diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/OCL/mitkPhotoacousticBModeFilter.h b/Modules/PhotoacousticsAlgorithms/Algorithms/OCL/mitkPhotoacousticBModeFilter.h deleted file mode 100644 index adc24614df..0000000000 --- a/Modules/PhotoacousticsAlgorithms/Algorithms/OCL/mitkPhotoacousticBModeFilter.h +++ /dev/null @@ -1,91 +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 _MITKPHOTOACOUSTICSOCLBEAMFORMER_H_ -#define _MITKPHOTOACOUSTICSOCLBEAMFORMER_H_ - -#include "mitkOclImageToImageFilter.h" -#include - -namespace mitk -{ - class OclImageToImageFilter; - - /** Documentation - * - * \brief The OclBinaryThresholdImageFilter computes a binary segmentation based on given - threshold values. - - * - * The filter requires two threshold values ( the upper and the lower threshold ) and two image values ( inside and outside ). The resulting voxel of the segmentation image is assigned the inside value 1 if the image value is between the given thresholds and the outside value otherwise. - */ - - - class PhotoacousticBModeFilter : public OclImageToImageFilter, public itk::Object - { - - public: - mitkClassMacroItkParent(PhotoacousticBModeFilter, itk::Object); - itkNewMacro(Self); - - /** - * @brief SetInput Set the input image. Only 3D images are supported for now. - * @param image a 3D image. - * @throw mitk::Exception if the dimesion is not 3. - */ - void SetInput(Image::Pointer image); - - /** Update the filter */ - void Update(); - - void SetParameters(bool useLogFilter) - { - m_UseLogFilter = useLogFilter; - } - - protected: - - /** Constructor */ - PhotoacousticBModeFilter(); - - /** Destructor */ - virtual ~PhotoacousticBModeFilter(); - - /** Initialize the filter */ - bool Initialize(); - - 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; - bool m_UseLogFilter; - }; -} -#endif \ No newline at end of file diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/OCL/mitkPhotoacousticOCLBeamformer.cpp b/Modules/PhotoacousticsAlgorithms/Algorithms/OCL/mitkPhotoacousticOCLBeamformer.cpp deleted file mode 100644 index 114810ddc9..0000000000 --- a/Modules/PhotoacousticsAlgorithms/Algorithms/OCL/mitkPhotoacousticOCLBeamformer.cpp +++ /dev/null @@ -1,177 +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. - -===================================================================*/ - -#include "mitkPhotoacousticOCLBeamformer.h" -#include "usServiceReference.h" - -mitk::PhotoacousticOCLBeamformer::PhotoacousticOCLBeamformer() -: m_PixelCalculation( NULL ) -{ - this->AddSourceFile("DASQuadratic.cl"); - this->AddSourceFile("DMASQuadratic.cl"); - this->AddSourceFile("DASspherical.cl"); - this->AddSourceFile("DMASspherical.cl"); - - this->m_FilterID = "PixelCalculation"; -} - -mitk::PhotoacousticOCLBeamformer::~PhotoacousticOCLBeamformer() -{ - if ( this->m_PixelCalculation ) - { - clReleaseKernel( m_PixelCalculation ); - } -} - -void mitk::PhotoacousticOCLBeamformer::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::PhotoacousticOCLBeamformer::Execute() -{ - cl_int clErr = 0; - - try - { - this->InitExec(this->m_PixelCalculation, m_OutputDim); - } - catch (const mitk::Exception& e) - { - MITK_ERROR << "Caught exception while initializing filter: " << e.what(); - return; - } - - if (m_Apodisation == nullptr) - { - MITK_INFO << "No apodisation function set; Beamforming will be done without any apodisation."; - m_Apodisation = new float[1]; - m_Apodisation[0] = 1; - m_ApodArraySize = 1; - } - - us::ServiceReference ref = GetModuleContext()->GetServiceReference(); - OclResourceService* resources = GetModuleContext()->GetService(ref); - cl_context gpuContext = resources->GetContext(); - - cl_mem cl_input = clCreateBuffer(gpuContext, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR, sizeof(float) * m_ApodArraySize, m_Apodisation, &clErr); - CHECK_OCL_ERR(clErr); - - // set kernel arguments - clErr = clSetKernelArg( this->m_PixelCalculation, 2, sizeof(cl_mem), &cl_input); - clErr |= clSetKernelArg( this->m_PixelCalculation, 3, sizeof(cl_ushort), &(this->m_ApodArraySize) ); - clErr |= clSetKernelArg( this->m_PixelCalculation, 4, sizeof(cl_float), &(this->m_SpeedOfSound) ); - clErr |= clSetKernelArg( this->m_PixelCalculation, 5, sizeof(cl_float), &(this->m_TimeSpacing) ); - clErr |= clSetKernelArg( this->m_PixelCalculation, 6, sizeof(cl_float), &(this->m_Pitch) ); - clErr |= clSetKernelArg( this->m_PixelCalculation, 7, sizeof(cl_float), &(this->m_Angle) ); - clErr |= clSetKernelArg( this->m_PixelCalculation, 8, sizeof(cl_ushort), &(this->m_PAImage)); - clErr |= clSetKernelArg(this->m_PixelCalculation, 9, sizeof(cl_ushort), &(this->m_TransducerElements)); - - CHECK_OCL_ERR( clErr ); - - // execute the filter on a 3D NDRange - this->ExecuteKernel( m_PixelCalculation, 3); - - // signalize the GPU-side data changed - m_Output->Modified( GPU_DATA ); -} - -us::Module *mitk::PhotoacousticOCLBeamformer::GetModule() -{ - return us::GetModuleContext()->GetModule(); -} - -bool mitk::PhotoacousticOCLBeamformer::Initialize() -{ - bool buildErr = true; - cl_int clErr = 0; - - if ( OclFilter::Initialize() ) - { - switch (m_Algorithm) - { - case BeamformingAlgorithm::DASQuad: - { - this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckDASQuad", &clErr); - break; - } - case BeamformingAlgorithm::DMASQuad: - { - this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckDMASQuad", &clErr); - break; - } - case BeamformingAlgorithm::DASSphe: - { - this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckDASSphe", &clErr); - break; - } - case BeamformingAlgorithm::DMASSphe: - { - this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckDMASSphe", &clErr); - break; - } - } - buildErr |= CHECK_OCL_ERR( clErr ); - } - return (OclFilter::IsInitialized() && buildErr ); -} - -void mitk::PhotoacousticOCLBeamformer::SetInput(mitk::Image::Pointer image) -{ - if(image->GetDimension() != 3) - { - mitkThrowException(mitk::Exception) << "Input for " << this->GetNameOfClass() << - " is not 3D. The filter only supports 3D. Please change your input."; - } - OclImageToImageFilter::SetInput(image); -} - -mitk::Image::Pointer mitk::PhotoacousticOCLBeamformer::GetOutput() -{ - if (m_Output->IsModified(GPU_DATA)) - { - void* pData = m_Output->TransferDataToCPU(m_CommandQue); - - const unsigned int dimension = 3; - unsigned int* dimensions = m_OutputDim; - - const mitk::SlicedGeometry3D::Pointer p_slg = m_Input->GetMITKImage()->GetSlicedGeometry(); - - MITK_DEBUG << "Creating new MITK Image."; - - m_Output->GetMITKImage()->Initialize(this->GetOutputType(), dimension, dimensions); - m_Output->GetMITKImage()->SetSpacing(p_slg->GetSpacing()); - m_Output->GetMITKImage()->SetGeometry(m_Input->GetMITKImage()->GetGeometry()); - m_Output->GetMITKImage()->SetImportVolume(pData, 0, 0, mitk::Image::ReferenceMemory); - } - - MITK_DEBUG << "Image Initialized."; - - return m_Output->GetMITKImage(); -} diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/OCL/mitkPhotoacousticOCLBeamformer.h b/Modules/PhotoacousticsAlgorithms/Algorithms/OCL/mitkPhotoacousticOCLBeamformer.h deleted file mode 100644 index 9a7c90e0de..0000000000 --- a/Modules/PhotoacousticsAlgorithms/Algorithms/OCL/mitkPhotoacousticOCLBeamformer.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 _MITKPHOTOACOUSTICSOCLBEAMFORMER_H_ -#define _MITKPHOTOACOUSTICSOCLBEAMFORMER_H_ - -#include "mitkOclImageToImageFilter.h" -#include - -namespace mitk -{ -class OclImageToImageFilter; - -/** Documentation - * - * \brief The OclBinaryThresholdImageFilter computes a binary segmentation based on given - threshold values. - - * - * The filter requires two threshold values ( the upper and the lower threshold ) and two image values ( inside and outside ). The resulting voxel of the segmentation image is assigned the inside value 1 if the image value is between the given thresholds and the outside value otherwise. - */ - - -class PhotoacousticOCLBeamformer : public OclImageToImageFilter, public itk::Object -{ - -public: - mitkClassMacroItkParent(PhotoacousticOCLBeamformer, itk::Object); - itkNewMacro(Self); - - /** - * @brief SetInput Set the input image. Only 3D images are supported for now. - * @param image a 3D image. - * @throw mitk::Exception if the dimesion is not 3. - */ - void SetInput(Image::Pointer image); - - mitk::Image::Pointer GetOutput(); - - /** Update the filter */ - void Update(); - - void SetOutputDim( unsigned int outputDim[3]) - { - m_OutputDim[0] = outputDim[0]; - m_OutputDim[1] = outputDim[1]; - m_OutputDim[2] = outputDim[2]; - } - - void SetApodisation(float* apodisation, unsigned short apodArraySize) - { - m_ApodArraySize = apodArraySize; - m_Apodisation = apodisation; - } - - enum BeamformingAlgorithm { DASQuad, DMASQuad, DASSphe, DMASSphe }; - - void SetAlgorithm(BeamformingAlgorithm algorithm, bool PA) - { - m_Algorithm = algorithm; - m_PAImage = PA; - } - - void SetBeamformingParameters(float SpeedOfSound, float timeSpacing, float Pitch, float Angle, bool PAImage, unsigned short transducerElements) - { - m_SpeedOfSound = SpeedOfSound; - m_TimeSpacing = timeSpacing; - m_Pitch = Pitch; - m_Angle = Angle; - m_PAImage = PAImage; - m_TransducerElements = transducerElements; - } - -protected: - - /** Constructor */ - PhotoacousticOCLBeamformer(); - - /** Destructor */ - virtual ~PhotoacousticOCLBeamformer(); - - /** Initialize the filter */ - bool Initialize(); - - 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; - BeamformingAlgorithm m_Algorithm; - unsigned short m_PAImage; - float m_SpeedOfSound; - float m_TimeSpacing; - float m_Pitch; - float m_Angle; - unsigned short m_TransducerElements; -}; -} -#endif \ No newline at end of file diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/mitkPhotoacousticBeamformingFilter.cpp b/Modules/PhotoacousticsAlgorithms/Algorithms/mitkPhotoacousticBeamformingFilter.cpp deleted file mode 100644 index 47587fb719..0000000000 --- a/Modules/PhotoacousticsAlgorithms/Algorithms/mitkPhotoacousticBeamformingFilter.cpp +++ /dev/null @@ -1,607 +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. - -===================================================================*/ - -#define _USE_MATH_DEFINES - -#include "mitkPhotoacousticBeamformingFilter.h" -#include "mitkProperties.h" -#include "mitkImageReadAccessor.h" -#include -#include -#include -#include -#include -#include -#include "mitkImageCast.h" -#include - - -mitk::BeamformingFilter::BeamformingFilter() : m_OutputData(nullptr), m_InputData(nullptr) -{ - this->SetNumberOfIndexedInputs(1); - this->SetNumberOfRequiredInputs(1); - - m_ProgressHandle = [](int, std::string) {}; -} - -void mitk::BeamformingFilter::SetProgressHandle(std::function progressHandle) -{ - m_ProgressHandle = progressHandle; -} - -mitk::BeamformingFilter::~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.ReconstructionLines, m_Conf.SamplesPerLine, input->GetDimension(2) }; - output->Initialize(mitk::MakeScalarPixelType(), 3, dim); - - mitk::Vector3D spacing; - spacing[0] = m_Conf.Pitch * m_Conf.TransducerElements * 1000 / m_Conf.ReconstructionLines; - spacing[1] = m_Conf.RecordTime / 2 * m_Conf.SpeedOfSound * 1000 / m_Conf.SamplesPerLine; - 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(); - mitk::Image::Pointer output = this->GetOutput(); - - if (!output->IsInitialized()) - return; - - float inputDim[2] = { (float)input->GetDimension(0), (float)input->GetDimension(1) }; - float outputDim[2] = { (float)output->GetDimension(0), (float)output->GetDimension(1) }; - - unsigned short chunkSize = 2; // TODO: make this slightly less arbitrary - - unsigned int oclOutputDim[3] = { output->GetDimension(0), output->GetDimension(1), output->GetDimension(2) }; - - unsigned int oclOutputDimChunk[3] = { output->GetDimension(0), output->GetDimension(1), chunkSize}; - unsigned int oclInputDimChunk[3] = { input->GetDimension(0), input->GetDimension(1), chunkSize}; - - unsigned int oclOutputDimLastChunk[3] = { output->GetDimension(0), output->GetDimension(1), input->GetDimension(2) % chunkSize }; - unsigned int oclInputDimLastChunk[3] = { input->GetDimension(0), input->GetDimension(1), input->GetDimension(2) % chunkSize }; - - const int apodArraySize = m_Conf.TransducerElements * 4; // set the resolution of the apodization array - float* ApodWindow; - - // calculate the appropiate apodization window - switch (m_Conf.Apod) - { - case beamformingSettings::Apodization::Hann: - ApodWindow = VonHannFunction(apodArraySize); - break; - case beamformingSettings::Apodization::Hamm: - ApodWindow = HammFunction(apodArraySize); - break; - case beamformingSettings::Apodization::Box: - ApodWindow = BoxFunction(apodArraySize); - break; - default: - ApodWindow = BoxFunction(apodArraySize); - break; - } - - int progInterval = output->GetDimension(2) / 20 > 1 ? output->GetDimension(2) / 20 : 1; - // the interval at which we update the gui progress bar - - auto begin = std::chrono::high_resolution_clock::now(); // debbuging the performance... - if (!m_Conf.UseGPU) - { - for (unsigned int i = 0; i < output->GetDimension(2); ++i) // seperate Slices should get Beamforming seperately applied - { - mitk::ImageReadAccessor inputReadAccessor(input, input->GetSliceData(i)); - - m_OutputData = new float[m_Conf.ReconstructionLines*m_Conf.SamplesPerLine]; - m_InputDataPuffer = new float[input->GetDimension(0)*input->GetDimension(1)]; - - // first, we convert any data to float, which we use by default - 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; - } - - // 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.Algorithm == beamformingSettings::BeamformingAlgorithm::DAS) - { - if (m_Conf.DelayCalculationMethod == beamformingSettings::DelayCalc::QuadApprox) - { - for (short line = 0; line < outputDim[0]; ++line) - { - threads[line] = std::thread(&BeamformingFilter::DASQuadraticLine, this, m_InputData, m_OutputData, inputDim, outputDim, line, ApodWindow, apodArraySize); - } - } - else if (m_Conf.DelayCalculationMethod == beamformingSettings::DelayCalc::Spherical) - { - for (short line = 0; line < outputDim[0]; ++line) - { - threads[line] = std::thread(&BeamformingFilter::DASSphericalLine, this, m_InputData, m_OutputData, inputDim, outputDim, line, ApodWindow, apodArraySize); - } - } - } - else if (m_Conf.Algorithm == beamformingSettings::BeamformingAlgorithm::DMAS) - { - if (m_Conf.DelayCalculationMethod == beamformingSettings::DelayCalc::QuadApprox) - { - for (short line = 0; line < outputDim[0]; ++line) - { - threads[line] = std::thread(&BeamformingFilter::DMASQuadraticLine, this, m_InputData, m_OutputData, inputDim, outputDim, line, ApodWindow, apodArraySize); - } - } - else if (m_Conf.DelayCalculationMethod == beamformingSettings::DelayCalc::Spherical) - { - for (short line = 0; line < outputDim[0]; ++line) - { - threads[line] = std::thread(&BeamformingFilter::DMASSphericalLine, this, m_InputData, m_OutputData, inputDim, outputDim, line, ApodWindow, apodArraySize); - } - } - } - // 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; - delete[] m_InputDataPuffer; - m_OutputData = nullptr; - m_InputData = nullptr; - } - } - else - { - mitk::PhotoacousticOCLBeamformer::Pointer m_oclFilter = mitk::PhotoacousticOCLBeamformer::New(); - - try - { - if (m_Conf.Algorithm == beamformingSettings::BeamformingAlgorithm::DAS) - { - if (m_Conf.DelayCalculationMethod == beamformingSettings::DelayCalc::QuadApprox) - m_oclFilter->SetAlgorithm(PhotoacousticOCLBeamformer::BeamformingAlgorithm::DASQuad, true); - else if (m_Conf.DelayCalculationMethod == beamformingSettings::DelayCalc::Spherical) - m_oclFilter->SetAlgorithm(PhotoacousticOCLBeamformer::BeamformingAlgorithm::DASSphe, true); - } - else if (m_Conf.Algorithm == beamformingSettings::BeamformingAlgorithm::DMAS) - { - if (m_Conf.DelayCalculationMethod == beamformingSettings::DelayCalc::QuadApprox) - m_oclFilter->SetAlgorithm(PhotoacousticOCLBeamformer::BeamformingAlgorithm::DMASQuad, true); - else if (m_Conf.DelayCalculationMethod == beamformingSettings::DelayCalc::Spherical) - m_oclFilter->SetAlgorithm(PhotoacousticOCLBeamformer::BeamformingAlgorithm::DMASSphe, true); - } - m_oclFilter->SetApodisation(ApodWindow, apodArraySize); - m_oclFilter->SetOutputDim(oclOutputDimChunk); - m_oclFilter->SetBeamformingParameters(m_Conf.SpeedOfSound, m_Conf.TimeSpacing, m_Conf.Pitch, m_Conf.Angle, m_Conf.Photoacoustic, m_Conf.TransducerElements); - - if (chunkSize < oclOutputDim[2]) - { - bool skip = false; - for (unsigned int i = 0; !skip && i < ceil((float)oclOutputDim[2] / (float)chunkSize); ++i) - { - m_ProgressHandle(100 * ((float)(i * chunkSize) / (float)oclOutputDim[2]), "performing reconstruction"); - mitk::Image::Pointer chunk = mitk::Image::New(); - if ((int)((oclOutputDim[2]) - (i * chunkSize)) == (int)(1 + chunkSize)) - { - // A 3d image of 3rd dimension == 1 can not be processed by openCL, make sure that this case never arises - oclInputDimLastChunk[2] = input->GetDimension(2) % chunkSize + chunkSize; - oclOutputDimLastChunk[2] = input->GetDimension(2) % chunkSize + chunkSize; - - chunk->Initialize(input->GetPixelType(), 3, oclInputDimLastChunk); - m_oclFilter->SetOutputDim(oclOutputDimLastChunk); - skip = true; //skip the last chunk - } - else if ((oclOutputDim[2]) - (i * chunkSize) >= chunkSize) - chunk->Initialize(input->GetPixelType(), 3, oclInputDimChunk); - else - { - chunk->Initialize(input->GetPixelType(), 3, oclInputDimLastChunk); - m_oclFilter->SetOutputDim(oclOutputDimLastChunk); - } - - chunk->SetSpacing(input->GetGeometry()->GetSpacing()); - - mitk::ImageReadAccessor ChunkMove(input); - chunk->SetImportVolume((void*)&(((float*)const_cast(ChunkMove.GetData()))[i * chunkSize * input->GetDimension(0) * input->GetDimension(1)]), 0, 0, mitk::Image::ReferenceMemory); - - m_oclFilter->SetInput(chunk); - m_oclFilter->Update(); - auto out = m_oclFilter->GetOutput(); - - for (unsigned int s = i * chunkSize; s < oclOutputDim[2]; ++s) // TODO: make the bounds here smaller... - { - mitk::ImageReadAccessor copy(out, out->GetSliceData(s - i * chunkSize)); - output->SetImportSlice(const_cast(copy.GetData()), s, 0, 0, mitk::Image::ReferenceMemory); - } - } - } - else - { - m_ProgressHandle(50, "performing reconstruction"); - - m_oclFilter->SetOutputDim(oclOutputDim); - m_oclFilter->SetInput(input); - m_oclFilter->Update(); - - auto out = m_oclFilter->GetOutput(); - mitk::ImageReadAccessor copy(out); - output->SetImportVolume(const_cast(copy.GetData()), 0, 0, mitk::Image::ReferenceMemory); - } - } - catch (mitk::Exception &e) - { - std::string errorMessage = "Caught unexpected exception "; - errorMessage.append(e.what()); - MITK_ERROR << errorMessage; - } - } - - 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; -} - -void mitk::BeamformingFilter::Configure(beamformingSettings settings) -{ - m_Conf = settings; -} - -float* mitk::BeamformingFilter::VonHannFunction(int samples) -{ - float* ApodWindow = new float[samples]; - - for (int n = 0; n < samples; ++n) - { - ApodWindow[n] = (1 - cos(2 * M_PI * n / (samples - 1))) / 2; - } - - return ApodWindow; -} - -float* mitk::BeamformingFilter::HammFunction(int samples) -{ - float* ApodWindow = new float[samples]; - - for (int n = 0; n < samples; ++n) - { - ApodWindow[n] = 0.54 - 0.46*cos(2 * M_PI*n / (samples - 1)); - } - - return ApodWindow; -} - -float* mitk::BeamformingFilter::BoxFunction(int samples) -{ - float* ApodWindow = new float[samples]; - - for (int n = 0; n < samples; ++n) - { - ApodWindow[n] = 1; - } - - return ApodWindow; -} - -void mitk::BeamformingFilter::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 * M_PI); - float part_multiplicator = tan_phi * m_Conf.TimeSpacing * m_Conf.SpeedOfSound / m_Conf.Pitch * m_Conf.ReconstructionLines / 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 = apodArraySize / (maxLine - minLine); - - 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.Photoacoustic)*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::BeamformingFilter::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 * M_PI); - float part_multiplicator = tan_phi * m_Conf.TimeSpacing * m_Conf.SpeedOfSound / m_Conf.Pitch * m_Conf.ReconstructionLines / 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 = apodArraySize / (maxLine - minLine); - - 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) * ((l_s - l_i)*m_Conf.Pitch*m_Conf.TransducerElements) / inputL), 2) - ) + (1 - m_Conf.Photoacoustic)*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::BeamformingFilter::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 * M_PI); - float part_multiplicator = tan_phi * m_Conf.TimeSpacing * m_Conf.SpeedOfSound / m_Conf.Pitch * m_Conf.ReconstructionLines / 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 = apodArraySize / (maxLine - minLine); - - 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.Photoacoustic)*s_i; - } - - for (short l_s1 = minLine; l_s1 < maxLine - 1; ++l_s1) - { - if (AddSample[l_s1 - minLine] < (short)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) - { - mult = input[l_s2 + AddSample[l_s2 - minLine] * (short)inputL] * apodisation[(short)((l_s2 - minLine)*apod_mult)] * input[l_s1 + AddSample[l_s1 - minLine] * (short)inputL] * apodisation[(short)((l_s1 - minLine)*apod_mult)]; - output[sample*(short)outputL + line] += sqrt(abs(mult)) * ((mult > 0) - (mult < 0)); - } - } - } - else - --usedLines; - } - - output[sample*(short)outputL + line] = 10 * output[sample*(short)outputL + line] / (pow(usedLines, 2) - (usedLines - 1)); - - delete[] AddSample; - } -} - -void mitk::BeamformingFilter::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 * M_PI); - float part_multiplicator = tan_phi * m_Conf.TimeSpacing * m_Conf.SpeedOfSound / m_Conf.Pitch * m_Conf.ReconstructionLines / m_Conf.TransducerElements; - float apod_mult = 1; - - float mult = 0; - - short usedLines = (maxLine - minLine); - - //exact 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 = apodArraySize / (maxLine - minLine); - - //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) * ((minLine + l_s - l_i)*m_Conf.Pitch*m_Conf.TransducerElements) / inputL), 2) - ) + (1 - m_Conf.Photoacoustic)*s_i; - } - - 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) - { - mult = input[l_s2 + AddSample[l_s2 - minLine] * (short)inputL] * apodisation[(int)((l_s2 - minLine)*apod_mult)] * input[l_s1 + AddSample[l_s1 - minLine] * (short)inputL] * apodisation[(int)((l_s1 - minLine)*apod_mult)]; - output[sample*(short)outputL + line] += sqrt(abs(mult)) * ((mult > 0) - (mult < 0)); - } - } - } - else - --usedLines; - } - - output[sample*(short)outputL + line] = 10 * output[sample*(short)outputL + line] / (pow(usedLines, 2) - (usedLines - 1)); - - delete[] AddSample; - } -} diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/mitkPhotoacousticBeamformingFilter.h b/Modules/PhotoacousticsAlgorithms/Algorithms/mitkPhotoacousticBeamformingFilter.h deleted file mode 100644 index e2654fc7fd..0000000000 --- a/Modules/PhotoacousticsAlgorithms/Algorithms/mitkPhotoacousticBeamformingFilter.h +++ /dev/null @@ -1,108 +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 MITK_PHOTOACOUSTICS_BEAMFORMING_FILTER -#define MITK_PHOTOACOUSTICS_BEAMFORMING_FILTER - -#include "mitkImageToImageFilter.h" -#include - -namespace mitk { - - //##Documentation - //## @brief - //## @ingroup Process - class BeamformingFilter : public ImageToImageFilter - { - public: - mitkClassMacro(BeamformingFilter, ImageToImageFilter); - - itkFactorylessNewMacro(Self) - itkCloneMacro(Self) - - struct beamformingSettings - { - float Pitch = 0.0003; // [m] - float SpeedOfSound = 1540; // [m/s] - unsigned int SamplesPerLine = 2048; - unsigned int ReconstructionLines = 128; - float RecordTime = 0.00006; // [s] - float TimeSpacing = 0.0000000000001; // [s] - unsigned int TransducerElements = 128; - bool partial = false; - unsigned int CropBounds[2] = { 0,0 }; - - bool UseGPU = true; - - enum DelayCalc {QuadApprox, Spherical}; - DelayCalc DelayCalculationMethod = QuadApprox; - - enum Apodization {Hamm, Hann, Box}; - Apodization Apod = Hann; - - enum BeamformingAlgorithm {DMAS, DAS}; - BeamformingAlgorithm Algorithm = DAS; - - float Angle = 10; - bool Photoacoustic = true; - float BPHighPass = 50; - float BPLowPass = 50; - bool UseBP = false; - }; - - void Configure(beamformingSettings settings); - - void SetProgressHandle(std::function progressHandle); - - protected: - - BeamformingFilter(); - - ~BeamformingFilter(); - - virtual void GenerateInputRequestedRegion() override; - - virtual void GenerateOutputInformation() override; - - virtual void GenerateData() override; - - //##Description - //## @brief Time when Header was last initialized - itk::TimeStamp m_TimeOfHeaderInitialization; - - std::function m_ProgressHandle; - - float* VonHannFunction(int samples); - float* HammFunction(int samples); - float* BoxFunction(int samples); - - void DASQuadraticLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, float* apodisation, const short& apodArraySize); - void DASSphericalLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, float* apodisation, const short& apodArraySize); - - void DMASQuadraticLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, float* apodisation, const short& apodArraySize); - void DMASSphericalLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, float* apodisation, const short& apodArraySize); - - float* m_OutputData; - float* m_InputData; - float* m_InputDataPuffer; - - beamformingSettings m_Conf; - }; - -} // namespace mitk - -#endif //MITK_PHOTOACOUSTICS_BEAMFORMING_FILTER diff --git a/Modules/PhotoacousticsAlgorithms/CMakeLists.txt b/Modules/PhotoacousticsAlgorithms/CMakeLists.txt index a1bd2a69cf..7b8587334b 100644 --- a/Modules/PhotoacousticsAlgorithms/CMakeLists.txt +++ b/Modules/PhotoacousticsAlgorithms/CMakeLists.txt @@ -1,8 +1,16 @@ +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 MitkCore MitkAlgorithmsExt MitkOpenCL + DEPENDS ${dependencies_list} #AUTOLOAD_WITH MitkCore INCLUDE_DIRS PUBLIC Algorithms/ITKUltrasound Algorithms Algorithms/OCL INTERNAL_INCLUDE_DIRS ${INCLUDE_DIRS_INTERNAL} PACKAGE_DEPENDS ITK|ITKFFT+ITKImageCompose+ITKImageIntensity -) +) \ No newline at end of file diff --git a/Modules/PhotoacousticsAlgorithms/Documentation/doxygen/PAModule.dox b/Modules/PhotoacousticsAlgorithms/Documentation/doxygen/PAModule.dox new file mode 100644 index 0000000000..342a21f696 --- /dev/null +++ b/Modules/PhotoacousticsAlgorithms/Documentation/doxygen/PAModule.dox @@ -0,0 +1,45 @@ +/** +\page PAModulePage The Photoacoustic Algorithms Module + +\tableofcontents + +\section PAModulePageOverview Overview + +The Photoacoustic Algorithms Module provides a set of filters for beamforming and post-processing of photoacoustic and ultrasound data. +The main features are: +
    +
  • Management of all filters through a single class PhotoacousticImage +
  • Beamforming of ultrasound and photoacoustic image data. +
      +
    • Beamforming using the DAS and DMAS Algorithms. +
    • Optional real-time beamforming capabilities by the usage of openCL GPU computing +
    +
  • Post/Pre-Processing of any kind of images. +
      +
    • Crop Filter for removing artefacts in upper and lower edge of the image. +
    • Multiple B-Mode Filter implementations with resampling and logarithmic filter. +
    • Bandpass Filter +
    +
+ +To use the GPU capabilities of this module, openCL needs to be activated in CMAKE. The custom build option "camiPhotoacousticsWorkstation" activates all needed CMAKE options, as well as openCL. +To build the project using openCL, the openCL libraries provided by your graphic card vendor need to be installed. The GPU capabilies of this module have been only tested using nvidia hardware, but, as openCL has been also implemented by AMD, this should work on either one. (Those are included in the CUDA package for nvidia graphic card owners) + +The \link org_mitk_gui_qt_photoacoustics_imageprocessing Photoacoustic Imageprocessing plugin \endlink provides a GUI to access all of thePhotoacoustic Algorithms Module's filters. + +\section PAModuleClasses The Photoacoustic Algorithms Module's Classes + +
    +
  • mitk::PhotoacousticImage: The class where all filters are managed. +
  • mitk::BeamformingSettings: The class used by many filters for storing the configuration to be used when applying them. +
  • Five filters are currently implemented in the Photoacoustic Algorithms module: +
      +
    • mitk::PhotoacousticBModeFilter/mitk::PhotoacousticOCLBModeFilter: Two classes for the B-Mode filter on GPU and CPU. +
    • Resampling Filter: A resampling filter for post-processing. +
    • mitk::BeamformingFilter: A filter with a switch for GPU/CPU computation, to compute the beamformed image out of raw ultrasound/photoacoustic data. +
    • Crop Filter: A filter for cropping artifacts on the upper and lower edges of the image. +
    • Bandpass Filter: A Filter to filter image data in the fourier domain, using a tukey window to cut off low or high frequency parts of the image. +
    +
    • +
+*/ \ No newline at end of file diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/LICENSE b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/LICENSE similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/LICENSE rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/LICENSE diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/README.rst b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/README.rst similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/README.rst rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/README.rst diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkAnalyticSignalImageFilter.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkAnalyticSignalImageFilter.h similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkAnalyticSignalImageFilter.h rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkAnalyticSignalImageFilter.h diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkAnalyticSignalImageFilter.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkAnalyticSignalImageFilter.hxx similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkAnalyticSignalImageFilter.hxx rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkAnalyticSignalImageFilter.hxx diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkBModeImageFilter.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkBModeImageFilter.h similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkBModeImageFilter.h rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkBModeImageFilter.h diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkBModeImageFilter.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkBModeImageFilter.hxx similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkBModeImageFilter.hxx rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkBModeImageFilter.hxx diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkCurvilinearArraySpecialCoordinatesImage.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkCurvilinearArraySpecialCoordinatesImage.h similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkCurvilinearArraySpecialCoordinatesImage.h rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkCurvilinearArraySpecialCoordinatesImage.h diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkCurvilinearArraySpecialCoordinatesImage.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkCurvilinearArraySpecialCoordinatesImage.hxx similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkCurvilinearArraySpecialCoordinatesImage.hxx rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkCurvilinearArraySpecialCoordinatesImage.hxx diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkFFT1DComplexConjugateToRealImageFilter.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DComplexConjugateToRealImageFilter.h similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkFFT1DComplexConjugateToRealImageFilter.h rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DComplexConjugateToRealImageFilter.h diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkFFT1DComplexConjugateToRealImageFilter.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DComplexConjugateToRealImageFilter.hxx similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkFFT1DComplexConjugateToRealImageFilter.hxx rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DComplexConjugateToRealImageFilter.hxx diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkFFT1DComplexToComplexImageFilter.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DComplexToComplexImageFilter.h similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkFFT1DComplexToComplexImageFilter.h rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DComplexToComplexImageFilter.h diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkFFT1DComplexToComplexImageFilter.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DComplexToComplexImageFilter.hxx similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkFFT1DComplexToComplexImageFilter.hxx rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DComplexToComplexImageFilter.hxx diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkFFT1DRealToComplexConjugateImageFilter.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DRealToComplexConjugateImageFilter.h similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkFFT1DRealToComplexConjugateImageFilter.h rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DRealToComplexConjugateImageFilter.h diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkFFT1DRealToComplexConjugateImageFilter.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DRealToComplexConjugateImageFilter.hxx similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkFFT1DRealToComplexConjugateImageFilter.hxx rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DRealToComplexConjugateImageFilter.hxx diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkRegionFromReferenceImageFilter.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkRegionFromReferenceImageFilter.h similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkRegionFromReferenceImageFilter.h rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkRegionFromReferenceImageFilter.h diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkRegionFromReferenceImageFilter.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkRegionFromReferenceImageFilter.hxx similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkRegionFromReferenceImageFilter.hxx rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkRegionFromReferenceImageFilter.hxx diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkSpectra1DImageFilter.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DImageFilter.h similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkSpectra1DImageFilter.h rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DImageFilter.h diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkSpectra1DImageFilter.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DImageFilter.hxx similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkSpectra1DImageFilter.hxx rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DImageFilter.hxx diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkSpectra1DSupportWindowImageFilter.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DSupportWindowImageFilter.h similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkSpectra1DSupportWindowImageFilter.h rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DSupportWindowImageFilter.h diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkSpectra1DSupportWindowImageFilter.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DSupportWindowImageFilter.hxx similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkSpectra1DSupportWindowImageFilter.hxx rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DSupportWindowImageFilter.hxx diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkSpectra1DSupportWindowToMaskImageFilter.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DSupportWindowToMaskImageFilter.h similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkSpectra1DSupportWindowToMaskImageFilter.h rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DSupportWindowToMaskImageFilter.h diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkSpectra1DSupportWindowToMaskImageFilter.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DSupportWindowToMaskImageFilter.hxx similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkSpectra1DSupportWindowToMaskImageFilter.hxx rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DSupportWindowToMaskImageFilter.hxx diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkTimeGainCompensationImageFilter.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkTimeGainCompensationImageFilter.h similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkTimeGainCompensationImageFilter.h rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkTimeGainCompensationImageFilter.h diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkTimeGainCompensationImageFilter.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkTimeGainCompensationImageFilter.hxx similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkTimeGainCompensationImageFilter.hxx rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkTimeGainCompensationImageFilter.hxx diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkVnlFFT1DComplexConjugateToRealImageFilter.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DComplexConjugateToRealImageFilter.h similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkVnlFFT1DComplexConjugateToRealImageFilter.h rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DComplexConjugateToRealImageFilter.h diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkVnlFFT1DComplexConjugateToRealImageFilter.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DComplexConjugateToRealImageFilter.hxx similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkVnlFFT1DComplexConjugateToRealImageFilter.hxx rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DComplexConjugateToRealImageFilter.hxx diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkVnlFFT1DComplexToComplexImageFilter.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DComplexToComplexImageFilter.h similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkVnlFFT1DComplexToComplexImageFilter.h rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DComplexToComplexImageFilter.h diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkVnlFFT1DComplexToComplexImageFilter.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DComplexToComplexImageFilter.hxx similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkVnlFFT1DComplexToComplexImageFilter.hxx rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DComplexToComplexImageFilter.hxx diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkVnlFFT1DRealToComplexConjugateImageFilter.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DRealToComplexConjugateImageFilter.h similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkVnlFFT1DRealToComplexConjugateImageFilter.h rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DRealToComplexConjugateImageFilter.h diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkVnlFFT1DRealToComplexConjugateImageFilter.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DRealToComplexConjugateImageFilter.hxx similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/ITKUltrasound/itkVnlFFT1DRealToComplexConjugateImageFilter.hxx rename to Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DRealToComplexConjugateImageFilter.hxx diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/itkPhotoacousticBModeImageFilter.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/itkPhotoacousticBModeImageFilter.h similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/itkPhotoacousticBModeImageFilter.h rename to Modules/PhotoacousticsAlgorithms/ITKFilter/itkPhotoacousticBModeImageFilter.h diff --git a/Modules/PhotoacousticsAlgorithms/Algorithms/itkPhotoacousticBModeImageFilter.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/itkPhotoacousticBModeImageFilter.hxx similarity index 100% rename from Modules/PhotoacousticsAlgorithms/Algorithms/itkPhotoacousticBModeImageFilter.hxx rename to Modules/PhotoacousticsAlgorithms/ITKFilter/itkPhotoacousticBModeImageFilter.hxx diff --git a/Modules/PhotoacousticsAlgorithms/Resources/BModeAbs.cl b/Modules/PhotoacousticsAlgorithms/Resources/BModeAbs.cl index ce692acbb6..5dfd66d02d 100644 --- a/Modules/PhotoacousticsAlgorithms/Resources/BModeAbs.cl +++ b/Modules/PhotoacousticsAlgorithms/Resources/BModeAbs.cl @@ -1,41 +1,38 @@ /*=================================================================== 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. ===================================================================*/ __kernel void ckBmodeAbs( - __read_only image3d_t dSource, // input image - __global float* dDest // output buffer + __global float* dSource, // input image + __global float* dDest, // output buffer + unsigned int size ) { // get thread identifier unsigned int globalPosX = get_global_id(0); unsigned int globalPosY = get_global_id(1); unsigned int globalPosZ = get_global_id(2); - // get image width and weight - const unsigned int inputL = get_image_width( dSource ); - const unsigned int inputS = get_image_height( dSource ); - const unsigned int Slices = get_image_depth( dSource ); - - // create an image sampler - const sampler_t defaultSampler = CLK_NORMALIZED_COORDS_FALSE | CLK_ADDRESS_CLAMP_TO_EDGE | CLK_FILTER_NEAREST ; + // get image width and height + unsigned short inputS = get_global_size(1); + unsigned short inputL = get_global_size(0); + unsigned short slices = get_global_size(2); // terminate non-valid threads - if ( globalPosX < inputL && globalPosY < inputS && globalPosZ < Slices ) + if ( globalPosX + inputL * globalPosY + inputL * inputS * globalPosZ < size ) { - - dDest[ globalPosZ * inputL * inputS + globalPosY * inputL + globalPosX ] = fabs(read_imagef( dSource, defaultSampler, (int4)(globalPosX, globalPosY, globalPosZ, 0 )).x); + dDest[ globalPosZ * inputL * inputS + globalPosY * inputL + globalPosX ] = fabs(dSource[ globalPosZ * inputL * inputS + globalPosY * inputL + globalPosX ]); } } \ No newline at end of file diff --git a/Modules/PhotoacousticsAlgorithms/Resources/BModeAbsLog.cl b/Modules/PhotoacousticsAlgorithms/Resources/BModeAbsLog.cl index 1daa1709e1..842e5a5b52 100644 --- a/Modules/PhotoacousticsAlgorithms/Resources/BModeAbsLog.cl +++ b/Modules/PhotoacousticsAlgorithms/Resources/BModeAbsLog.cl @@ -1,40 +1,38 @@ /*=================================================================== 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. ===================================================================*/ __kernel void ckBmodeAbsLog( - __read_only image3d_t dSource, // input image - __global float* dDest // output buffer + __global float* dSource, // input image + __global float* dDest, // output buffer + unsigned int size ) { // get thread identifier unsigned int globalPosX = get_global_id(0); unsigned int globalPosY = get_global_id(1); unsigned int globalPosZ = get_global_id(2); - // get image width and weight - const unsigned int inputL = get_image_width( dSource ); - const unsigned int inputS = get_image_height( dSource ); - const unsigned int Slices = get_image_depth( dSource ); - - // create an image sampler - const sampler_t defaultSampler = CLK_NORMALIZED_COORDS_FALSE | CLK_ADDRESS_CLAMP_TO_EDGE | CLK_FILTER_NEAREST ; + // get image width and height + unsigned short inputS = get_global_size(1); + unsigned short inputL = get_global_size(0); + unsigned short slices = get_global_size(2); // terminate non-valid threads - if ( globalPosX < inputL && globalPosY < inputS && globalPosZ < Slices ) + if ( globalPosX + inputL * globalPosY + inputL * inputS * globalPosZ < size ) { - dDest[ globalPosZ * inputL * inputS + globalPosY * inputL + globalPosX ] = log(fabs((float)read_imagef( dSource, defaultSampler, (int4)(globalPosX, globalPosY, globalPosZ, 0 )).x)); + dDest[ globalPosZ * inputL * inputS + globalPosY * inputL + globalPosX ] = log(fabs(dSource[ globalPosZ * inputL * inputS + globalPosY * inputL + globalPosX ])); } } \ No newline at end of file diff --git a/Modules/PhotoacousticsAlgorithms/Resources/DAS.cl b/Modules/PhotoacousticsAlgorithms/Resources/DAS.cl new file mode 100644 index 0000000000..2540ec58db --- /dev/null +++ b/Modules/PhotoacousticsAlgorithms/Resources/DAS.cl @@ -0,0 +1,64 @@ +/*=================================================================== + +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. + +===================================================================*/ + +__kernel void ckDAS( + __global float* dSource, // input image + __global float* dDest, // output buffer + __global unsigned short* usedLines, + __global unsigned short* delays, + __constant float* apodArray, + unsigned short apodArraySize, + unsigned int inputL, + unsigned int inputS, + unsigned int Slices, + unsigned int outputL, + unsigned int outputS // parameters +) +{ + // get thread identifier + unsigned int globalPosX = get_global_id(0); + unsigned int globalPosY = get_global_id(1); + unsigned int globalPosZ = get_global_id(2); + + // terminate non-valid threads + if ( globalPosX < outputL && globalPosY < outputS && globalPosZ < Slices ) + { + float l_i = (float)globalPosX / (float)outputL * (float)inputL; + + unsigned short curUsedLines = usedLines[globalPosY * 3 * outputL + 3 * globalPosX]; + unsigned short minLine = usedLines[globalPosY * 3 * outputL + 3 * globalPosX + 1]; + unsigned short maxLine = usedLines[globalPosY * 3 *outputL + 3 * globalPosX + 2]; + + float apod_mult = (float)apodArraySize / (float)curUsedLines; + + unsigned short Delay = 0; + + float output = 0; + float mult = 0; + + for (short l_s = minLine; l_s < maxLine; ++l_s) + { + Delay = delays[globalPosY * (outputL / 2) + (int)(fabs(l_s - l_i)/(float)inputL * (float)outputL)]; + if (Delay < inputS && Delay >= 0) { + output += apodArray[(int)((l_s - minLine)*apod_mult)] * dSource[(int)(globalPosZ * inputL * inputS + Delay * inputL + l_s)]; + } + else + --curUsedLines; + } + + dDest[ globalPosZ * outputL * outputS + globalPosY * outputL + globalPosX ] = output / (float)curUsedLines; + } +} \ No newline at end of file diff --git a/Modules/PhotoacousticsAlgorithms/Resources/DASQuadratic.cl b/Modules/PhotoacousticsAlgorithms/Resources/DASQuadratic.cl deleted file mode 100644 index 8afda8ff42..0000000000 --- a/Modules/PhotoacousticsAlgorithms/Resources/DASQuadratic.cl +++ /dev/null @@ -1,76 +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. - -===================================================================*/ - -__kernel void ckDASQuad( - __read_only image3d_t dSource, // input image - __global float* dDest, // output buffer - __global float* apodArray, - unsigned short apodArraySize, - float SpeedOfSound, - float TimeSpacing, - float Pitch, - float Angle, - unsigned short PAImage, - unsigned short TransducerElements // parameters -) -{ - // get thread identifier - unsigned int globalPosX = get_global_id(0); - unsigned int globalPosY = get_global_id(1); - unsigned int globalPosZ = get_global_id(2); - - unsigned short outputS = get_global_size(1); - unsigned short outputL = get_global_size(0); - - // get image width and weight - const unsigned int inputL = get_image_width( dSource ); - const unsigned int inputS = get_image_height( dSource ); - const unsigned int Slices = get_image_depth( dSource ); - - // create an image sampler - const sampler_t defaultSampler = CLK_NORMALIZED_COORDS_FALSE | CLK_ADDRESS_CLAMP_TO_EDGE | CLK_FILTER_NEAREST ; - - // terminate non-valid threads - if ( globalPosX < outputL && globalPosY < outputS && globalPosZ < Slices ) - { - float l_i = (float)globalPosX / outputL * inputL; - float s_i = (float)globalPosY / outputS * inputS / 2; - - float part = (tan(Angle / 360 * 2 * M_PI) * TimeSpacing * SpeedOfSound / Pitch * outputL / TransducerElements) * s_i; - if (part < 1) - part = 1; - - short maxLine = min((l_i + part) + 1, (float)inputL); - short minLine = max((l_i - part), 0.0f); - short usedLines = (maxLine - minLine); - float apod_mult = apodArraySize / (maxLine - minLine); - - short AddSample = 0; - float output = 0; - float delayMultiplicator = pow(1 / (TimeSpacing*SpeedOfSound) * Pitch * 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-PAImage)*s_i; - if (AddSample < inputS && AddSample >= 0) - output += apodArray[(short)((l_s - minLine)*apod_mult)] * read_imagef( dSource, defaultSampler, (int4)(l_s, AddSample, globalPosZ, 0 )).x; - else - --usedLines; - } - - dDest[ globalPosZ * outputL * outputS + globalPosY * outputL + globalPosX ] = output / usedLines; - } -} \ No newline at end of file diff --git a/Modules/PhotoacousticsAlgorithms/Resources/DASspherical.cl b/Modules/PhotoacousticsAlgorithms/Resources/DASspherical.cl deleted file mode 100644 index f9a11f7504..0000000000 --- a/Modules/PhotoacousticsAlgorithms/Resources/DASspherical.cl +++ /dev/null @@ -1,79 +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. - -===================================================================*/ - -__kernel void ckDASSphe( - __read_only image3d_t dSource, // input image - __global float* dDest, // output buffer - __global float* apodArray, - unsigned short apodArraySize, - float SpeedOfSound, - float TimeSpacing, - float Pitch, - float Angle, - unsigned short PAImage, - unsigned short TransducerElements // parameters -) -{ - // get thread identifier - unsigned int globalPosX = get_global_id(0); - unsigned int globalPosY = get_global_id(1); - unsigned int globalPosZ = get_global_id(2); - - unsigned short outputS = get_global_size(1); - unsigned short outputL = get_global_size(0); - - // get image width and weight - const unsigned int inputL = get_image_width( dSource ); - const unsigned int inputS = get_image_height( dSource ); - const unsigned int Slices = get_image_depth( dSource ); - - // create an image sampler - const sampler_t defaultSampler = CLK_NORMALIZED_COORDS_FALSE | CLK_ADDRESS_CLAMP_TO_EDGE | CLK_FILTER_NEAREST ; - - // terminate non-valid threads - if ( globalPosX < outputL && globalPosY < outputS && globalPosZ < Slices ) - { - float l_i = (float)globalPosX / outputL * inputL; - float s_i = (float)globalPosY / outputS * inputS / 2; - - float part = (tan(Angle / 360 * 2 * M_PI) * TimeSpacing * SpeedOfSound / Pitch * outputL / TransducerElements) * s_i; - if (part < 1) - part = 1; - - short maxLine = min((l_i + part) + 1, (float)inputL); - short minLine = max((l_i - part), 0.0f); - short usedLines = (maxLine - minLine); - float apod_mult = apodArraySize / (maxLine - minLine); - - short AddSample = 0; - float output = 0; - - for (short l_s = minLine; l_s < maxLine; ++l_s) - { - AddSample = sqrt( - pow(s_i, 2) - + - pow((1 / (TimeSpacing*SpeedOfSound) * ((l_s - l_i)*Pitch*TransducerElements) / inputL), 2) - ) + (1-PAImage)*s_i; - if (AddSample < inputS && AddSample >= 0) - output += apodArray[(short)((l_s - minLine)*apod_mult)] * read_imagef( dSource, defaultSampler, (int4)(l_s, AddSample, globalPosZ, 0 )).x; - else - --usedLines; - } - - dDest[ globalPosZ * outputL * outputS + globalPosY * outputL + globalPosX ] = output / usedLines; - } -} \ No newline at end of file diff --git a/Modules/PhotoacousticsAlgorithms/Resources/DMAS.cl b/Modules/PhotoacousticsAlgorithms/Resources/DMAS.cl new file mode 100644 index 0000000000..89cc58bf12 --- /dev/null +++ b/Modules/PhotoacousticsAlgorithms/Resources/DMAS.cl @@ -0,0 +1,85 @@ +/*=================================================================== + +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. + +===================================================================*/ + +__kernel void ckDMAS( + __global float* dSource, // input image + __global float* dDest, // output buffer + __global unsigned short* usedLines, + __global unsigned short* AddSamples, + __constant float* apodArray, + unsigned short apodArraySize, + unsigned int inputL, + unsigned int inputS, + unsigned int Slices, + unsigned int outputL, + unsigned int outputS // parameters +) +{ + // get thread identifier + unsigned int globalPosX = get_global_id(0); + unsigned int globalPosY = get_global_id(1); + unsigned int globalPosZ = get_global_id(2); + + // terminate non-valid threads + if ( globalPosX < outputL && globalPosY < outputS && globalPosZ < Slices ) + { + float l_i = (float)globalPosX / (float)outputL * (float)inputL; + + unsigned short curUsedLines = usedLines[globalPosY * 3 * outputL + 3 * globalPosX]; + unsigned short minLine = usedLines[globalPosY * 3 * outputL + 3 * globalPosX + 1]; + unsigned short maxLine = usedLines[globalPosY * 3 *outputL + 3 * globalPosX + 2]; + + float apod_mult = (float)apodArraySize / (float)curUsedLines; + + unsigned short Delay1 = 0; + unsigned short Delay2 = 0; + + float output = 0; + float mult = 0; + + float s_1 = 0; + float s_2 = 0; + float apod_1 = 0; + + for (short l_s1 = minLine; l_s1 < maxLine; ++l_s1) + { + Delay1 = AddSamples[globalPosY * (outputL / 2) + (int)(fabs(l_s1 - l_i)/(float)inputL * (float)outputL)]; + if (Delay1 < inputS && Delay1 >= 0) + { + s_1 = dSource[(int)(globalPosZ * inputL * inputS + Delay1 * inputL + l_s1)]; + apod_1 = apodArray[(int)((l_s1 - minLine)*apod_mult)]; + + for (short l_s2 = l_s1 + 1; l_s2 < maxLine; ++l_s2) + { + Delay2 = AddSamples[globalPosY * (outputL / 2) + (int)(fabs(l_s2 - l_i)/(float)inputL * (float)outputL)]; + if (Delay2 < inputS && Delay2 >= 0) + { + s_2 = dSource[(int)(globalPosZ * inputL * inputS + Delay2 * inputL + l_s2)]; + + mult = apodArray[(int)((l_s2 - minLine)*apod_mult)] * s_2 + * apod_1 * s_1; + + output += sqrt(fabs(mult)) * ((mult > 0) - (mult < 0)); + } + } + } + else + --curUsedLines; + } + + dDest[ globalPosZ * outputL * outputS + globalPosY * outputL + globalPosX ] = output / (float)(curUsedLines * curUsedLines - (curUsedLines - 1)); + } +} diff --git a/Modules/PhotoacousticsAlgorithms/Resources/DMASQuadratic.cl b/Modules/PhotoacousticsAlgorithms/Resources/DMASQuadratic.cl deleted file mode 100644 index 857b988746..0000000000 --- a/Modules/PhotoacousticsAlgorithms/Resources/DMASQuadratic.cl +++ /dev/null @@ -1,92 +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. - -===================================================================*/ - -__kernel void ckDMASQuad( - __read_only image3d_t dSource, // input image - __global float* dDest, // output buffer - __global float* apodArray, - unsigned short apodArraySize, - float SpeedOfSound, - float TimeSpacing, - float Pitch, - float Angle, - unsigned short PAImage, - unsigned short TransducerElements // parameters -) -{ - // get thread identifier - unsigned int globalPosX = get_global_id(0); - unsigned int globalPosY = get_global_id(1); - unsigned int globalPosZ = get_global_id(2); - - unsigned short outputS = get_global_size(1); - unsigned short outputL = get_global_size(0); - - // get image width and weight - const unsigned int inputL = get_image_width( dSource ); - const unsigned int inputS = get_image_height( dSource ); - const unsigned int Slices = get_image_depth( dSource ); - - // create an image sampler - const sampler_t defaultSampler = CLK_NORMALIZED_COORDS_FALSE | CLK_ADDRESS_CLAMP_TO_EDGE | CLK_FILTER_NEAREST ; - - // terminate non-valid threads - if ( globalPosX < outputL && globalPosY < outputS && globalPosZ < Slices ) - { - float l_i = (float)globalPosX / outputL * inputL; - float s_i = (float)globalPosY / outputS * inputS / 2; - - float part = (tan(Angle / 360 * 2 * M_PI) * TimeSpacing * SpeedOfSound / Pitch * outputL / TransducerElements) * s_i; - if (part < 1) - part = 1; - - short maxLine = min((l_i + part) + 1, (float)inputL); - short minLine = max((l_i - part), 0.0f); - short usedLines = (maxLine - minLine); - float apod_mult = apodArraySize / (maxLine - minLine); - - float delayMultiplicator = pow((1 / (TimeSpacing*SpeedOfSound) * Pitch * TransducerElements / inputL), 2) / s_i / 2; - - float mult = 0; - float output = 0; - float AddSample1 = 0; - float AddSample2 = 0; - - for (short l_s1 = minLine; l_s1 < maxLine - 1; ++l_s1) - { - AddSample1 = delayMultiplicator * pow((l_s1 - l_i), 2) + s_i + (1-PAImage)*s_i; - if (AddSample1 < inputS && AddSample1 >= 0) - { - for (short l_s2 = l_s1 + 1; l_s2 < maxLine; ++l_s2) - { - AddSample2 = delayMultiplicator * pow((l_s2 - l_i), 2) + s_i + (1-PAImage)*s_i; - if (AddSample2 < inputS && AddSample2 >= 0) - { - mult = read_imagef( dSource, defaultSampler, (int4)(l_s2, AddSample2, globalPosZ, 0 )).x - * apodArray[(short)((l_s2 - minLine)*apod_mult)] - * read_imagef( dSource, defaultSampler, (int4)(l_s1, AddSample1, globalPosZ, 0 )).x - * apodArray[(short)((l_s1 - minLine)*apod_mult)]; - output += sqrt(mult * ((float)(mult>0)-(float)(mult<0))) * ((mult > 0) - (mult < 0)); - } - } - } - else - --usedLines; - } - - dDest[ globalPosZ * outputL * outputS + globalPosY * outputL + globalPosX ] = 10 * output / (pow((float)usedLines, 2.0f) - (usedLines - 1)); - } -} \ No newline at end of file diff --git a/Modules/PhotoacousticsAlgorithms/Resources/DMASspherical.cl b/Modules/PhotoacousticsAlgorithms/Resources/DMASspherical.cl deleted file mode 100644 index fc480b0820..0000000000 --- a/Modules/PhotoacousticsAlgorithms/Resources/DMASspherical.cl +++ /dev/null @@ -1,98 +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. - -===================================================================*/ - -__kernel void ckDMASSphe( - __read_only image3d_t dSource, // input image - __global float* dDest, // output buffer - __global float* apodArray, - unsigned short apodArraySize, - float SpeedOfSound, - float TimeSpacing, - float Pitch, - float Angle, - unsigned short PAImage, - unsigned short TransducerElements // parameters -) -{ - // get thread identifier - unsigned int globalPosX = get_global_id(0); - unsigned int globalPosY = get_global_id(1); - unsigned int globalPosZ = get_global_id(2); - - unsigned short outputS = get_global_size(1); - unsigned short outputL = get_global_size(0); - - // get image width and weight - const unsigned int inputL = get_image_width( dSource ); - const unsigned int inputS = get_image_height( dSource ); - const unsigned int Slices = get_image_depth( dSource ); - - // create an image sampler - const sampler_t defaultSampler = CLK_NORMALIZED_COORDS_FALSE | CLK_ADDRESS_CLAMP_TO_EDGE | CLK_FILTER_NEAREST ; - - // terminate non-valid threads - if ( globalPosX < outputL && globalPosY < outputS && globalPosZ < Slices ) - { - float l_i = (float)globalPosX / outputL * inputL; - float s_i = (float)globalPosY / outputS * inputS / 2; - - float part = (tan(Angle / 360 * 2 * M_PI) * TimeSpacing * SpeedOfSound / Pitch * outputL / TransducerElements) * s_i; - if (part < 1) - part = 1; - - short maxLine = min((l_i + part) + 1, (float)inputL); - short minLine = max((l_i - part), 0.0f); - short usedLines = (maxLine - minLine); - float apod_mult = apodArraySize / (maxLine - minLine); - - float mult = 0; - float output = 0; - float AddSample1 = 0; - float AddSample2 = 0; - - for (short l_s1 = minLine; l_s1 < maxLine - 1; ++l_s1) - { - AddSample1 = sqrt( - pow(s_i, 2) - + - pow((1 / (TimeSpacing*SpeedOfSound) * ((l_s1 - l_i)*Pitch*TransducerElements)/inputL), 2) - ) + (1-PAImage)*s_i; - if (AddSample1 < inputS && AddSample1 >= 0) - { - for (short l_s2 = l_s1 + 1; l_s2 < maxLine; ++l_s2) - { - AddSample2 = sqrt( - pow(s_i, 2) - + - pow((1 / (TimeSpacing*SpeedOfSound) * ((l_s2 - l_i)*Pitch*TransducerElements)/inputL), 2) - ) + (1-PAImage)*s_i; - if (AddSample2 < inputS && AddSample2 >= 0) - { - mult = read_imagef( dSource, defaultSampler, (int4)(l_s2, AddSample2, globalPosZ, 0 )).x - * apodArray[(short)((l_s2 - minLine)*apod_mult)] - * read_imagef( dSource, defaultSampler, (int4)(l_s1, AddSample1, globalPosZ, 0 )).x - * apodArray[(short)((l_s1 - minLine)*apod_mult)]; - output += sqrt(mult * ((float)(mult>0)-(float)(mult<0))) * ((mult > 0) - (mult < 0)); - } - } - } - else - --usedLines; - } - - dDest[ globalPosZ * outputL * outputS + globalPosY * outputL + globalPosX ] = 10 * output / (pow((float)usedLines, 2.0f) - (usedLines - 1)); - } -} \ No newline at end of file diff --git a/Modules/PhotoacousticsAlgorithms/Resources/DelayCalculation.cl b/Modules/PhotoacousticsAlgorithms/Resources/DelayCalculation.cl new file mode 100644 index 0000000000..0be471b2b4 --- /dev/null +++ b/Modules/PhotoacousticsAlgorithms/Resources/DelayCalculation.cl @@ -0,0 +1,69 @@ +/*=================================================================== + +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. + +===================================================================*/ + +__kernel void ckDelayCalculationQuad( __global unsigned short *gDest, + __global unsigned short *usedLines, + unsigned int inputL, + unsigned int inputS, + unsigned int outputL, + unsigned int outputS, + char isPAImage, + float delayMultiplicatorRaw // parameters + ) +{ + uint globalPosX = get_global_id(0); + uint globalPosY = get_global_id(1); + + if (globalPosX * 2 < outputL && globalPosY < outputS) + { + float l_i = 0; // we calculate the delays relative to line zero + float s_i = (float)globalPosY / (float)outputS * (float)inputS / 2; + + float l_s = (float)globalPosX / (float)outputL * (float)inputL; // the currently calculated line + + float delayMultiplicator = delayMultiplicatorRaw / s_i; + gDest[globalPosY * (outputL / 2) + globalPosX] = delayMultiplicator * pow((l_s - l_i), 2) + s_i + (1-isPAImage)*s_i; + } +} + +__kernel void ckDelayCalculationSphe( __global unsigned short *gDest, + __global unsigned short *usedLines, + unsigned int inputL, + unsigned int inputS, + unsigned int outputL, + unsigned int outputS, + char isPAImage, + float delayMultiplicatorRaw // parameters + ) +{ + uint globalPosX = get_global_id(0); + uint globalPosY = get_global_id(1); + + if (globalPosX * 2 < outputL && globalPosY < outputS) + { + float l_i = 0; // we calculate the delays relative to line zero + float s_i = (float)globalPosY / (float)outputS * (float)inputS / 2; + + float l_s = (float)globalPosX / (float)outputL * (float)inputL; // the currently calculated line + + gDest[globalPosY * (outputL / 2) + globalPosX] = + sqrt( + pow(s_i, 2) + + + pow((delayMultiplicatorRaw * ((l_s - l_i)) / inputL), 2) + ) + (1-isPAImage)*s_i; + } +} \ No newline at end of file diff --git a/Modules/PhotoacousticsAlgorithms/Resources/UsedLinesCalculation.cl b/Modules/PhotoacousticsAlgorithms/Resources/UsedLinesCalculation.cl new file mode 100644 index 0000000000..638de2b279 --- /dev/null +++ b/Modules/PhotoacousticsAlgorithms/Resources/UsedLinesCalculation.cl @@ -0,0 +1,50 @@ +/*=================================================================== + +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. + +===================================================================*/ + +__kernel void ckUsedLines( + __global unsigned short* dDest, // output buffer + float partMult, + unsigned int inputL, + unsigned int inputS, + unsigned int outputL, + unsigned int outputS +) +{ + // get thread identifier + unsigned int globalPosX = get_global_id(0); + unsigned int globalPosY = get_global_id(1); + + //unsigned short outputS = get_global_size(1); + //unsigned short outputL = get_global_size(0); + + // terminate non-valid threads + if ( globalPosX < outputL && globalPosY < outputS) + { + float l_i = (float)globalPosX / outputL * inputL; + float s_i = (float)globalPosY / outputS * inputS / 2; + + float part = partMult * s_i; + if (part < 1) + part = 1; + + unsigned short maxLine = min((l_i + part) + 1, (float)inputL); + unsigned short minLine = max((l_i - part), 0.0f); + + dDest[globalPosY * 3 * outputL + 3 * globalPosX] = (maxLine - minLine); //usedLines + dDest[globalPosY * 3 * outputL + 3 * globalPosX + 1] = minLine; //minLine + dDest[globalPosY * 3 * outputL + 3 * globalPosX + 2] = maxLine; //maxLine + } +} \ No newline at end of file diff --git a/Modules/PhotoacousticsAlgorithms/Resources/sDMAS.cl b/Modules/PhotoacousticsAlgorithms/Resources/sDMAS.cl new file mode 100644 index 0000000000..b362047846 --- /dev/null +++ b/Modules/PhotoacousticsAlgorithms/Resources/sDMAS.cl @@ -0,0 +1,87 @@ +/*=================================================================== + +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. + +===================================================================*/ + +__kernel void cksDMAS( + __global float* dSource, // input image + __global float* dDest, // output buffer + __global unsigned short* usedLines, + __global unsigned short* AddSamples, + __constant float* apodArray, + unsigned short apodArraySize, + unsigned int inputL, + unsigned int inputS, + unsigned int Slices, + unsigned int outputL, + unsigned int outputS // parameters +) +{ + // get thread identifier + unsigned int globalPosX = get_global_id(0); + unsigned int globalPosY = get_global_id(1); + unsigned int globalPosZ = get_global_id(2); + + // terminate non-valid threads + if ( globalPosX < outputL && globalPosY < outputS && globalPosZ < Slices ) + { + float l_i = (float)globalPosX / (float)outputL * (float)inputL; + + unsigned short curUsedLines = usedLines[globalPosY * 3 * outputL + 3 * globalPosX]; + unsigned short minLine = usedLines[globalPosY * 3 * outputL + 3 * globalPosX + 1]; + unsigned short maxLine = usedLines[globalPosY * 3 *outputL + 3 * globalPosX + 2]; + + float apod_mult = (float)apodArraySize / (float)curUsedLines; + + unsigned short Delay1 = 0; + unsigned short Delay2 = 0; + + float output = 0; + float mult = 0; + + float s_1 = 0; + float s_2 = 0; + float sign = 0; + float apod_1 = 0; + + for (short l_s1 = minLine; l_s1 < maxLine; ++l_s1) + { + Delay1 = AddSamples[globalPosY * (outputL / 2) + (int)(fabs(l_s1 - l_i)/(float)inputL * (float)outputL)]; + if (Delay1 < inputS && Delay1 >= 0) + { + s_1 = dSource[(int)(globalPosZ * inputL * inputS + Delay1 * inputL + l_s1)]; + apod_1 = apodArray[(int)((l_s1 - minLine)*apod_mult)]; + sign += s_1; + + for (short l_s2 = l_s1 + 1; l_s2 < maxLine; ++l_s2) + { + Delay2 = AddSamples[globalPosY * (outputL / 2) + (int)(fabs(l_s2 - l_i)/(float)inputL * (float)outputL)]; + if (Delay2 < inputS && Delay2 >= 0) + { + s_2 = dSource[(int)(globalPosZ * inputL * inputS + Delay2 * inputL + l_s2)]; + + mult = apodArray[(int)((l_s2 - minLine)*apod_mult)] * s_2 + * apod_1 * s_1; + + output += sqrt(fabs(mult)) * ((mult > 0) - (mult < 0)); + } + } + } + else + --curUsedLines; + } + + dDest[ globalPosZ * outputL * outputS + globalPosY * outputL + globalPosX ] = output / (float)(curUsedLines * curUsedLines - (curUsedLines - 1)) * ((sign > 0) - (sign < 0)); + } +} diff --git a/Modules/PhotoacousticsAlgorithms/files.cmake b/Modules/PhotoacousticsAlgorithms/files.cmake index 08f72362af..ac29b12402 100644 --- a/Modules/PhotoacousticsAlgorithms/files.cmake +++ b/Modules/PhotoacousticsAlgorithms/files.cmake @@ -1,18 +1,20 @@ +file(GLOB_RECURSE H_FILES RELATIVE "${CMAKE_CURRENT_SOURCE_DIR}" "${CMAKE_CURRENT_SOURCE_DIR}/include/*") + set(CPP_FILES - mitkPhotoacousticImage.cpp - - Algorithms/mitkPhotoacousticBeamformingFilter.cpp - - Algorithms/OCL/mitkPhotoacousticOCLBeamformer.cpp - - Algorithms/OCL/mitkPhotoacousticBModeFilter.cpp + source/mitkPhotoacousticImage.cpp + source/mitkPhotoacousticBeamformingFilter.cpp + source/OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.cpp + source/OpenCLFilter/mitkPhotoacousticBModeFilter.cpp + source/OpenCLFilter/mitkPhotoacousticOCLUsedLinesCalculation.cpp + source/OpenCLFilter/mitkPhotoacousticOCLDelayCalculation.cpp ) set(RESOURCE_FILES - DASQuadratic.cl - DMASQuadratic.cl - DASspherical.cl - DMASspherical.cl BModeAbs.cl BModeAbsLog.cl -) \ No newline at end of file + UsedLinesCalculation.cl + DelayCalculation.cl + DMAS.cl + DAS.cl + sDMAS.cl +) diff --git a/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticBModeFilter.h b/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticBModeFilter.h new file mode 100644 index 0000000000..aa98d0fc37 --- /dev/null +++ b/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticBModeFilter.h @@ -0,0 +1,140 @@ +/*=================================================================== + +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 _MITKPHOTOACOUSTICSBMODEFILTER_H_ +#define _MITKPHOTOACOUSTICSBMODEFILTER_H_ + +#if defined(PHOTOACOUSTICS_USE_GPU) || DOXYGEN +#include "mitkOclDataSetToDataSetFilter.h" +#endif + +#include +#include "mitkImageToImageFilter.h" + +namespace mitk +{ + #if defined(PHOTOACOUSTICS_USE_GPU) || DOXYGEN + + /*! + * \brief Class implementing a mitk::OclDataSetToDataSetFilter for BMode filtering on GPU + * + * The only parameter that needs to be provided is whether it should use a logfilter. + * Currently this class only performs an absolute BMode filter. + */ + class PhotoacousticOCLBModeFilter : public OclDataSetToDataSetFilter, public itk::Object + { + + public: + mitkClassMacroItkParent(PhotoacousticOCLBModeFilter, itk::Object); + itkNewMacro(Self); + + /** \brief Set the input image to be processed + */ + void SetInput(Image::Pointer image); + + void Update(); + + /** \brief Set parameters for the filter + * + * @param useLogFilter If true, the filter will apply a logfilter on the processed image + */ + void SetParameters(bool useLogFilter) + { + m_UseLogFilter = useLogFilter; + } + + /** + * @brief GetOutput Returns an mitk::Image constructed from the processed data + */ + mitk::Image::Pointer GetOutput(); + + protected: + + PhotoacousticOCLBModeFilter(); + + virtual ~PhotoacousticOCLBModeFilter(); + + bool Initialize(); + + 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; + bool m_UseLogFilter; + + mitk::Image::Pointer m_InputImage; + unsigned int m_InputDim[3]; + unsigned int m_Size; + + }; + #endif + + /*! + * \brief Class implementing a mitk::ImageToImageFilter for BMode filtering on CPU + * + * The only parameter that needs to be provided is whether it should use a logfilter. + * Currently this class only performs an absolute BMode filter. + */ + class PhotoacousticBModeFilter : public ImageToImageFilter + { + public: + mitkClassMacro(PhotoacousticBModeFilter, ImageToImageFilter); + + itkFactorylessNewMacro(Self) + itkCloneMacro(Self) + + /** \brief Set parameters for the filter + * + * @param useLogFilter If true, the filter will apply a logfilter on the processed image + */ + void SetParameters(bool useLogFilter) + { + m_UseLogFilter = useLogFilter; + } + + protected: + + PhotoacousticBModeFilter(); + + ~PhotoacousticBModeFilter(); + + virtual void GenerateInputRequestedRegion() override; + + virtual void GenerateOutputInformation() override; + + virtual void GenerateData() override; + + //##Description + //## @brief Time when Header was last initialized + itk::TimeStamp m_TimeOfHeaderInitialization; + + bool m_UseLogFilter; + }; +} +#endif diff --git a/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.h b/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.h new file mode 100644 index 0000000000..885223739d --- /dev/null +++ b/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.h @@ -0,0 +1,152 @@ +/*=================================================================== + +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 + +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); + itkNewMacro(Self); + + /** + * @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; + } + + /** \brief Set beamforming settings to use when beamforming */ + void SetConfig(BeamformingSettings settings) + { + m_ConfOld = m_Conf; + m_Conf = settings; + } + +protected: + + PhotoacousticOCLBeamformingFilter(); + 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 m_Conf; + BeamformingSettings m_ConfOld; + + 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 +class PhotoacousticOCLBeamformingFilter : public itk::Object +{ +public: + mitkClassMacroItkParent(mitk::PhotoacousticOCLBeamformingFilter, itk::Object); + itkNewMacro(Self); + +protected: + /** Constructor */ + PhotoacousticOCLBeamformingFilter() {} + + /** Destructor */ + virtual ~PhotoacousticOCLBeamformingFilter() {} +}; +} +#endif +#endif diff --git a/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticOCLDelayCalculation.h b/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticOCLDelayCalculation.h new file mode 100644 index 0000000000..061f7c7448 --- /dev/null +++ b/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticOCLDelayCalculation.h @@ -0,0 +1,99 @@ +/*=================================================================== + +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" + +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); + itkNewMacro(Self); + + void Update(); + + /** \brief Sets a new configuration to use. + * + * @param conf The configuration set to use for the calculation of the delays. + */ + void SetConfig(BeamformingSettings conf) + { + m_Conf = conf; + } + + /** \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(); + 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 m_Conf; + cl_mem m_UsedLines; + unsigned int m_BufferSize; + float m_DelayMultiplicatorRaw; + char m_IsPAImage; + size_t m_ChunkSize[3]; + }; +} +#endif +#endif \ No newline at end of file diff --git a/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticOCLUsedLinesCalculation.h b/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticOCLUsedLinesCalculation.h new file mode 100644 index 0000000000..e787d2009a --- /dev/null +++ b/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticOCLUsedLinesCalculation.h @@ -0,0 +1,90 @@ +/*=================================================================== + +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" + +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); + itkNewMacro(Self); + + void Update(); + + /** \brief Sets a new configuration to use. + * + * @param conf The configuration set to use for the calculation of the used lines. + */ + void SetConfig(BeamformingSettings conf) + { + m_Conf = conf; + } + + protected: + + /** Constructor */ + OCLUsedLinesCalculation(); + + /** 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 m_Conf; + float m_part; + size_t m_ChunkSize[3]; + }; +} +#endif +#endif diff --git a/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticBeamformingFilter.h b/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticBeamformingFilter.h new file mode 100644 index 0000000000..214ef84e5d --- /dev/null +++ b/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticBeamformingFilter.h @@ -0,0 +1,151 @@ +/*=================================================================== + +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" + +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); + + itkFactorylessNewMacro(Self) + itkCloneMacro(Self) + + /** \brief Sets a new configuration to use + * + * @param settings The configuration set to use for beamforming + */ + void Configure(BeamformingSettings settings) + { + m_ConfOld = m_Conf; + m_Conf = settings; + } + + /** \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(); + + ~BeamformingFilter(); + + virtual void GenerateInputRequestedRegion() override; + + virtual void GenerateOutputInformation() override; + + virtual 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; + + /** \brief Pointer holding the Von-Hann apodization window for beamforming + * @param samples the resolution at which the window is created + */ + float* VonHannFunction(int samples); + /** \brief Function to create a Hamming apodization window + * @param samples the resolution at which the window is created + */ + float* HammFunction(int samples); + /** \brief Function to create a Box apodization window + * @param samples the resolution at which the window is created + */ + float* BoxFunction(int samples); + + /** \brief Function to perform beamforming on CPU for a single line, using DAS and quadratic delay + */ + void DASQuadraticLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, float* apodisation, const short& apodArraySize); + /** \brief Function to perform beamforming on CPU for a single line, using DAS and spherical delay + */ + void DASSphericalLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, float* apodisation, const short& apodArraySize); + /** \brief Function to perform beamforming on CPU for a single line, using DMAS and quadratic delay + */ + void DMASQuadraticLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, float* apodisation, const short& apodArraySize); + /** \brief Function to perform beamforming on CPU for a single line, using DMAS and spherical delay + */ + void DMASSphericalLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, float* apodisation, const short& apodArraySize); + /** \brief Function to perform beamforming on CPU for a single line, using signed DMAS and quadratic delay + */ + void sDMASQuadraticLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, float* apodisation, const short& apodArraySize); + /** \brief Function to perform beamforming on CPU for a single line, using signed DMAS and spherical delay + */ + void sDMASSphericalLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, float* apodisation, const short& apodArraySize); + + float* m_OutputData; + float* m_InputData; + float* m_InputDataPuffer; + + /** \brief Pointer holding the Von-Hann apodization window for beamforming + */ + float* m_VonHannFunction; + /** \brief Pointer holding the Hamming apodization window for beamforming + */ + float* m_HammFunction; + /** \brief Pointer holding the Box apodization window for beamforming + */ + float* m_BoxFunction; + + /** \brief Current configuration set + */ + BeamformingSettings m_Conf; + /** \brief Previous configuration set to selectively update used data for beamforming + */ + BeamformingSettings m_ConfOld; + + /** \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/mitkPhotoacousticBeamformingSettings.h new file mode 100644 index 0000000000..a48b5e78a3 --- /dev/null +++ b/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticBeamformingSettings.h @@ -0,0 +1,137 @@ +/*=================================================================== + +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 + + + +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: + /** \brief Pitch of the used transducer in [m]. + */ + float Pitch = 0.0003; + /** \brief Speed of sound in the used medium in [m/s]. + */ + float SpeedOfSound = 1540; + /** \brief This parameter is not neccessary to be set, as it's never used. + */ + float RecordTime = 0.00006; // [s] + /** \brief The time spacing of the input image + */ + float TimeSpacing = 0.0000000000001; // [s] + /** \brief The angle of the transducer elements + */ + float Angle = -1; + /** \brief Flag whether processed image is a photoacoustic image or an ultrasound image + */ + bool isPhotoacousticImage = true; + + /** \brief How many transducer elements the used transducer had. + */ + unsigned short TransducerElements = 128; + /** \brief How many vertical samples should be used in the final image. + */ + unsigned int SamplesPerLine = 2048; + /** \brief How many lines should be reconstructed in the final image. + */ + unsigned int 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 upperCutoff = 0; + /** \brief Sets whether only the slices selected by mitk::BeamformingSettings::CropBounds should be beamformed. + */ + bool partial = false; + /** \brief Sets the first and last slice to be beamformed. + */ + unsigned int CropBounds[2] = { 0,0 }; + /** \brief Sets the dimensions of the inputImage. + */ + unsigned int inputDim[3] = { 1,1,1 }; + + /** \brief Decides whether GPU computing should be used + */ + bool UseGPU = true; + + /** \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 Sets how the delays for beamforming should be calculated. + */ + DelayCalc DelayCalculationMethod = QuadApprox; + + /** \brief Available apodization functions: + * - Hamming function. + * - Von-Hann function. + * - Box function. + */ + enum Apodization { Hamm, Hann, Box }; + /** \brief Sets the used apodization function. + */ + Apodization Apod = Hann; + /** \brief Sets the resolution of the apodization array (must be greater than 0). + */ + int apodizationArraySize = 128; + + /** \brief Available beamforming algorithms: + * - DAS (Delay and sum). + * - DMAS (Delay multiply and sum). + */ + enum BeamformingAlgorithm { DMAS, DAS, sDMAS}; + /** \brief Sets the used beamforming algorithm. + */ + BeamformingAlgorithm Algorithm = DAS; + + /** \brief Sets whether after beamforming a bandpass should be automatically applied + */ + bool UseBP = false; + /** \brief Sets the position at which lower frequencies are completely cut off in Hz. + */ + float BPHighPass = 50; + /** \brief Sets the position at which higher frequencies are completely cut off in Hz. + */ + float BPLowPass = 50; + + /** \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& lhs, const BeamformingSettings& rhs) + { + return !((abs(lhs.Angle - rhs.Angle) < 0.01f) && // 0.01 degree error margin + (lhs.Apod == rhs.Apod) && + (lhs.DelayCalculationMethod == rhs.DelayCalculationMethod) && + (lhs.isPhotoacousticImage == rhs.isPhotoacousticImage) && + (abs(lhs.Pitch - rhs.Pitch) < 0.000001f) && // 0.0001 mm error margin + (lhs.ReconstructionLines == rhs.ReconstructionLines) && + (abs(lhs.RecordTime - rhs.RecordTime) < 0.00000001f) && // 10 ns error margin + (lhs.SamplesPerLine == rhs.SamplesPerLine) && + (abs(lhs.SpeedOfSound - rhs.SpeedOfSound) < 0.01f) && + (abs(lhs.TimeSpacing - rhs.TimeSpacing) < 0.00000000001f) && //0.01 ns error margin + (lhs.TransducerElements == rhs.TransducerElements)); + } + }; +} +#endif \ No newline at end of file diff --git a/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticImage.h b/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticImage.h new file mode 100644 index 0000000000..b92fb58ade --- /dev/null +++ b/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticImage.h @@ -0,0 +1,125 @@ +/*=================================================================== + +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 alpha); + + protected: + PhotoacousticImage(); + virtual ~PhotoacousticImage(); + + /** \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); + }; +} // namespace mitk + +#endif /* mitkPhotoacousticImage_H_HEADER_INCLUDED */ diff --git a/Modules/PhotoacousticsAlgorithms/mitkPhotoacousticImage.cpp b/Modules/PhotoacousticsAlgorithms/mitkPhotoacousticImage.cpp index 9ba451e9cd..08f92552bc 100644 --- a/Modules/PhotoacousticsAlgorithms/mitkPhotoacousticImage.cpp +++ b/Modules/PhotoacousticsAlgorithms/mitkPhotoacousticImage.cpp @@ -1,641 +1,522 @@ /*=================================================================== 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 "mitkPhotoacousticImage.h" -#include "itkBModeImageFilter.h" -#include "itkPhotoacousticBModeImageFilter.h" +#include "ITKFilter/ITKUltrasound/itkBModeImageFilter.h" +#include "ITKFilter/itkPhotoacousticBModeImageFilter.h" #include "mitkImageCast.h" #include "mitkITKImageImport.h" #include "mitkPhotoacousticBeamformingFilter.h" #include #include -#include +#include "./OpenCLFilter/mitkPhotoacousticBModeFilter.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 "itkFFT1DComplexConjugateToRealImageFilter.h" -#include "itkFFT1DRealToComplexConjugateImageFilter.h" +#include "ITKFilter/ITKUltrasound/itkFFT1DComplexConjugateToRealImageFilter.h" +#include "ITKFilter/ITKUltrasound/itkFFT1DRealToComplexConjugateImageFilter.h" mitk::PhotoacousticImage::PhotoacousticImage() { MITK_INFO << "[PhotoacousticImage Debug] created that image"; } mitk::PhotoacousticImage::~PhotoacousticImage() { MITK_INFO << "[PhotoacousticImage Debug] destroyed that image"; } -mitk::Image::Pointer mitk::PhotoacousticImage::ApplyBmodeFilter(mitk::Image::Pointer inputImage, BModeMethod method, bool UseLogFilter, float resampleSpacing) +mitk::Image::Pointer mitk::PhotoacousticImage::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) { - auto input = ApplyCropping(inputImage, 0, 0, 0, 0, 0, inputImage->GetDimension(2) - 1); - PhotoacousticBModeFilter::Pointer filter = PhotoacousticBModeFilter::New(); - filter->SetParameters(UseLogFilter); - filter->SetInput(input); - filter->Update(); + 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(); - auto out = filter->GetOutput(); + out = filter->GetOutput(); - if(resampleSpacing == 0) - return out; + 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::ShapeDetection) { 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::PhotoacousticImage::ApplyScatteringCompensation(mitk::Image::Pointer inputImage, int scattering) { typedef itk::Image< float, 3 > itkFloatImageType; typedef itk::MultiplyImageFilter MultiplyImageFilterType; itkFloatImageType::Pointer itkImage; mitk::CastToItkImage(inputImage, itkImage); MultiplyImageFilterType::Pointer multiplyFilter = MultiplyImageFilterType::New(); multiplyFilter->SetInput1(itkImage); multiplyFilter->SetInput2(m_FluenceCompResizedItk.at(m_ScatteringCoefficient)); return mitk::GrabItkImageMemory(multiplyFilter->GetOutput()); }*/ mitk::Image::Pointer mitk::PhotoacousticImage::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::PhotoacousticImage::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 those float, short, float are used at all... though it's easy to add other ones 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 unsigned shorto 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 unsigned shorto 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::ReferenceMemory); return output; } -mitk::Image::Pointer mitk::PhotoacousticImage::ApplyBeamforming(mitk::Image::Pointer inputImage, BeamformingFilter::beamformingSettings config, int cutoff, std::function progressHandle) +mitk::Image::Pointer mitk::PhotoacousticImage::ApplyBeamforming(mitk::Image::Pointer inputImage, BeamformingSettings config, int cutoff, std::function progressHandle) { - // crop the image - // set the Maximum Size of the image to 4096 - unsigned short lowerCutoff = 0; - if (((unsigned int)(4096 + cutoff)) < inputImage->GetDimension(1)) - { - lowerCutoff = (unsigned short)(inputImage->GetDimension(1) - 4096); - } - - config.RecordTime = config.RecordTime - (cutoff + lowerCutoff) / inputImage->GetDimension(1) * config.RecordTime; // adjust the recorded time lost by cropping + config.RecordTime = config.RecordTime - (cutoff) / inputImage->GetDimension(1) * config.RecordTime; // adjust the recorded time lost by cropping progressHandle(0, "cropping image"); if (!config.partial) { config.CropBounds[0] = 0; config.CropBounds[1] = inputImage->GetDimension(2) - 1; } - Image::Pointer processedImage = ApplyCropping(inputImage, cutoff, lowerCutoff, 0, 0, config.CropBounds[0], config.CropBounds[1]); - - // resample the image in horizontal direction - if (inputImage->GetDimension(0) != config.ReconstructionLines) - { - progressHandle(0, "resampling image"); - auto begin = std::chrono::high_resolution_clock::now(); - unsigned int dim[2] = { config.ReconstructionLines, processedImage->GetDimension(1) }; - processedImage = ApplyResampling(processedImage, dim); - auto end = std::chrono::high_resolution_clock::now(); - MITK_DEBUG << "Upsampling from " << inputImage->GetDimension(0) << " to " << config.ReconstructionLines << " lines completed in " << ((double)std::chrono::duration_cast(end - begin).count()) / 1000000 << "ms" << std::endl; - } + Image::Pointer processedImage = ApplyCropping(inputImage, cutoff, 0, 0, 0, config.CropBounds[0], config.CropBounds[1]); + config.inputDim[0] = processedImage->GetDimension(0); + config.inputDim[1] = processedImage->GetDimension(1); + config.inputDim[2] = processedImage->GetDimension(2); // perform the beamforming BeamformingFilter::Pointer Beamformer = BeamformingFilter::New(); Beamformer->SetInput(processedImage); Beamformer->Configure(config); Beamformer->SetProgressHandle(progressHandle); Beamformer->UpdateLargestPossibleRegion(); processedImage = Beamformer->GetOutput(); return processedImage; } mitk::Image::Pointer mitk::PhotoacousticImage::BandpassFilter(mitk::Image::Pointer data, float recordTime, float BPHighPass, float BPLowPass, float alpha) { 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, alpha); 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::PhotoacousticImage::BPFunction(mitk::Image::Pointer reference, int cutoffFrequencyPixelHighPass, int cutoffFrequencyPixelLowPass, float alpha) { float* imageData = new float[reference->GetDimension(0)*reference->GetDimension(1)]; // tukey window float width = reference->GetDimension(1) / 2 - (float)cutoffFrequencyPixelHighPass - (float)cutoffFrequencyPixelLowPass; float center = (float)cutoffFrequencyPixelHighPass / 2 + width / 2; MITK_INFO << width << "width " << center << "center " << alpha; for (unsigned int n = 0; n < reference->GetDimension(1); ++n) { imageData[reference->GetDimension(0)*n] = 0; } for (int n = 0; n < width; ++n) { if (n <= (alpha*(width - 1)) / 2) { imageData[reference->GetDimension(0)*(int)(n + center - (width / 2))] = (1 + cos(M_PI*(2 * n / (alpha*(width - 1)) - 1))) / 2; } else if (n >= (width - 1)*(1 - alpha / 2) && n <= (width - 1)) { imageData[reference->GetDimension(0)*(int)(n + center - (width / 2))] = (1 + cos(M_PI*(2 * n / (alpha*(width - 1)) + 1 - 2 / alpha))) / 2; } else { imageData[reference->GetDimension(0)*(int)(n + center - (width / 2))] = 1; } } // Butterworth-Filter /* // first, write the HighPass if (cutoffFrequencyPixelHighPass != reference->GetDimension(1) / 2) { for (int n = 0; n < reference->GetDimension(1) / 2; ++n) { imageData[reference->GetDimension(0)*n] = 1 / (1 + pow( (float)n / (float)(reference->GetDimension(1) / 2 - cutoffFrequencyPixelHighPass) , 2 * butterworthOrder)); } } else { for (int n = 0; n < reference->GetDimension(1) / 2; ++n) { imageData[reference->GetDimension(0)*n] = 1; } } // now, the LowPass for (int n = 0; n < reference->GetDimension(1) / 2; ++n) { imageData[reference->GetDimension(0)*n] *= 1 / (1 + pow( (float)(reference->GetDimension(1) / 2 - 1 - n) / (float)(reference->GetDimension(1) / 2 - cutoffFrequencyPixelLowPass) , 2 * butterworthOrder)); } */ // 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 (ImageType::IndexValueType slice = 0; slice < reference->GetDimension(2); ++slice) { for (ImageType::IndexValueType line = 0; line < reference->GetDimension(0); ++line) { for (ImageType::IndexValueType 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; -} - - -/* -mitk::CropFilter::CropFilter() - : m_PixelCalculation(NULL) -{ - this->AddSourceFile("CropFilter.cl"); - - this->m_FilterID = "CropFilter"; -} - -mitk::CropFilter::~CropFilter() -{ - if (this->m_PixelCalculation) - { - clReleaseKernel(m_PixelCalculation); - } -} - -void mitk::CropFilter::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::CropFilter::Execute() -{ - cl_int clErr = 0; - - try - { - this->InitExec(this->m_PixelCalculation); - } - catch (const mitk::Exception& e) - { - MITK_ERROR << "Catched exception while initializing filter: " << e.what(); - return; - } - - us::ServiceReference ref = GetModuleContext()->GetServiceReference(); - OclResourceService* resources = GetModuleContext()->GetService(ref); - cl_context gpuContext = resources->GetContext(); - - unsigned int size = m_OutputDim[0] * m_OutputDim[1] * m_OutputDim[2] * m_Images; - - cl_mem cl_input = clCreateBuffer(gpuContext, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR, sizeof(float) * size, m_Data, &clErr); - CHECK_OCL_ERR(clErr); - - // set kernel arguments - clErr = clSetKernelArg(this->m_PixelCalculation, 2, sizeof(cl_mem), &cl_input); - clErr |= clSetKernelArg(this->m_PixelCalculation, 3, sizeof(cl_ushort), &(this->m_Images)); - - CHECK_OCL_ERR(clErr); - - // execute the filter on a 3D NDRange - this->ExecuteKernel(m_PixelCalculation, 3); - - // signalize the GPU-side data changed - m_Output->Modified(GPU_DATA); -} - -us::Module *mitk::CropFilter::GetModule() -{ - return us::GetModuleContext()->GetModule(); -} - -bool mitk::CropFilter::Initialize() -{ - bool buildErr = true; - cl_int clErr = 0; - - if (OclFilter::Initialize()) - { - this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckCrop", &clErr); - buildErr |= CHECK_OCL_ERR(clErr); - } - return (OclFilter::IsInitialized() && buildErr); -} - -void mitk::CropFilter::SetInput(mitk::Image::Pointer image) -{ - if (image->GetDimension() != 3) - { - mitkThrowException(mitk::Exception) << "Input for " << this->GetNameOfClass() << - " is not 3D. The filter only supports 3D. Please change your input."; - } - OclImageToImageFilter::SetInput(image); -} - -mitk::Image::Pointer mitk::CropFilter::GetOutput() -{ - if (m_Output->IsModified(GPU_DATA)) - { - void* pData = m_Output->TransferDataToCPU(m_CommandQue); - - const unsigned int dimension = 3; - unsigned int* dimensions = m_OutputDim; - - const mitk::SlicedGeometry3D::Pointer p_slg = m_Input->GetMITKImage()->GetSlicedGeometry(); - - MITK_DEBUG << "Creating new MITK Image."; - - m_Output->GetMITKImage()->Initialize(this->GetOutputType(), dimension, dimensions); - m_Output->GetMITKImage()->SetSpacing(p_slg->GetSpacing()); - m_Output->GetMITKImage()->SetGeometry(m_Input->GetMITKImage()->GetGeometry()); - m_Output->GetMITKImage()->SetImportVolume(pData, 0, 0, mitk::Image::ReferenceMemory); - } - - MITK_DEBUG << "Image Initialized."; - - return m_Output->GetMITKImage(); -} - -*/ +} \ No newline at end of file diff --git a/Modules/PhotoacousticsAlgorithms/mitkPhotoacousticImage.h b/Modules/PhotoacousticsAlgorithms/mitkPhotoacousticImage.h index daab4a43cf..2200124e8d 100644 --- a/Modules/PhotoacousticsAlgorithms/mitkPhotoacousticImage.h +++ b/Modules/PhotoacousticsAlgorithms/mitkPhotoacousticImage.h @@ -1,53 +1,50 @@ /*=================================================================== 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 "mitkOclImageToImageFilter.h" #include "mitkPhotoacousticBeamformingFilter.h" - #include "MitkPhotoacousticsAlgorithmsExports.h" namespace mitk { class MITKPHOTOACOUSTICSALGORITHMS_EXPORT PhotoacousticImage : public itk::Object { public: mitkClassMacroItkParent(mitk::PhotoacousticImage, itk::Object); itkFactorylessNewMacro(Self); enum BModeMethod { ShapeDetection, Abs }; - mitk::Image::Pointer ApplyBmodeFilter(mitk::Image::Pointer inputImage, BModeMethod method = BModeMethod::Abs, bool UseLogFilter = false, float resampleSpacing = 0.15); + 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); mitk::Image::Pointer ApplyResampling(mitk::Image::Pointer inputImage, unsigned int outputSize[2]); - mitk::Image::Pointer ApplyBeamforming(mitk::Image::Pointer inputImage, BeamformingFilter::beamformingSettings config, int cutoff, std::function progressHandle = [](int, std::string) {}); + mitk::Image::Pointer ApplyBeamforming(mitk::Image::Pointer inputImage, BeamformingSettings config, int cutoff, std::function progressHandle = [](int, std::string) {}); mitk::Image::Pointer ApplyCropping(mitk::Image::Pointer inputImage, int above, int below, int right, int left, int minSlice, int maxSlice); mitk::Image::Pointer BandpassFilter(mitk::Image::Pointer data, float recordTime, float BPHighPass, float BPLowPass, float alpha); protected: PhotoacousticImage(); virtual ~PhotoacousticImage(); itk::Image::Pointer BPFunction(mitk::Image::Pointer reference, int cutoffFrequencyPixelHighPass, int cutoffFrequencyPixelLowPass, float alpha); }; } // namespace mitk #endif /* mitkPhotoacousticImage_H_HEADER_INCLUDED */ diff --git a/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticBModeFilter.cpp b/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticBModeFilter.cpp new file mode 100644 index 0000000000..f9db6a7105 --- /dev/null +++ b/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticBModeFilter.cpp @@ -0,0 +1,221 @@ +/*=================================================================== + +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 "./OpenCLFilter/mitkPhotoacousticBModeFilter.h" +#include "usServiceReference.h" +#include + +#if defined(PHOTOACOUSTICS_USE_GPU) || DOXYGEN + +mitk::PhotoacousticOCLBModeFilter::PhotoacousticOCLBModeFilter() + : m_PixelCalculation(NULL) +{ + this->AddSourceFile("BModeAbs.cl"); + this->AddSourceFile("BModeAbsLog.cl"); + + this->m_FilterID = "BModeFilter"; + + this->Initialize(); +} + +mitk::PhotoacousticOCLBModeFilter::~PhotoacousticOCLBModeFilter() +{ + if (this->m_PixelCalculation) + { + clReleaseKernel(m_PixelCalculation); + } +} + +void mitk::PhotoacousticOCLBModeFilter::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::PhotoacousticOCLBModeFilter::Execute() +{ + try + { + size_t outputSize = m_InputDim[0] * m_InputDim[1] * m_InputDim[2]; + this->InitExec(this->m_PixelCalculation, m_InputDim, outputSize, sizeof(float)); + } + catch (const mitk::Exception& e) + { + MITK_ERROR << "Catched exception while initializing filter: " << e.what(); + return; + } + + cl_int clErr; + clErr = clSetKernelArg(this->m_PixelCalculation, 2, sizeof(cl_uint), &(this->m_Size)); + + CHECK_OCL_ERR(clErr); + + // execute the filter on a 3D NDRange + this->ExecuteKernel(m_PixelCalculation, 3); + + // signalize the GPU-side data changed + m_Output->Modified(GPU_DATA); +} + +us::Module *mitk::PhotoacousticOCLBModeFilter::GetModule() +{ + return us::GetModuleContext()->GetModule(); +} + +bool mitk::PhotoacousticOCLBModeFilter::Initialize() +{ + bool buildErr = true; + cl_int clErr = 0; + + if (OclFilter::Initialize()) + { + if(m_UseLogFilter) + this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckBmodeAbsLog", &clErr); + else + this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckBmodeAbs", &clErr); + buildErr |= CHECK_OCL_ERR(clErr); + } + return (OclFilter::IsInitialized() && buildErr); +} + +void mitk::PhotoacousticOCLBModeFilter::SetInput(mitk::Image::Pointer image) +{ + OclDataSetToDataSetFilter::SetInput(image); + + m_InputImage = image; + m_InputDim[0] = m_InputImage->GetDimension(0); + m_InputDim[1] = m_InputImage->GetDimension(1); + m_InputDim[2] = m_InputImage->GetDimension(2); + m_Size = m_InputDim[0] * m_InputDim[1] * m_InputDim[2]; +} + +mitk::Image::Pointer mitk::PhotoacousticOCLBModeFilter::GetOutput() +{ + mitk::Image::Pointer outputImage = mitk::Image::New(); + + if (m_Output->IsModified(GPU_DATA)) + { + void* pData = m_Output->TransferDataToCPU(m_CommandQue); + + const unsigned int dimension = 3; + unsigned int dimensions[3] = { m_InputDim[0], m_InputDim[1], m_InputDim[2] }; + + const mitk::SlicedGeometry3D::Pointer p_slg = m_InputImage->GetSlicedGeometry(); + + MITK_DEBUG << "Creating new MITK Image."; + + outputImage->Initialize(this->GetOutputType(), dimension, dimensions); + outputImage->SetSpacing(p_slg->GetSpacing()); + outputImage->SetGeometry(m_InputImage->GetGeometry()); + outputImage->SetImportVolume(pData, 0, 0, mitk::Image::ReferenceMemory); + } + + MITK_DEBUG << "Image Initialized."; + + return outputImage; +} + +#endif + + +mitk::PhotoacousticBModeFilter::PhotoacousticBModeFilter() : m_UseLogFilter(false) +{ + this->SetNumberOfIndexedInputs(1); + this->SetNumberOfRequiredInputs(1); +} + +mitk::PhotoacousticBModeFilter::~PhotoacousticBModeFilter() +{ +} + +void mitk::PhotoacousticBModeFilter::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::PhotoacousticBModeFilter::GenerateOutputInformation() +{ + mitk::Image::ConstPointer input = this->GetInput(); + mitk::Image::Pointer output = this->GetOutput(); + + if ((output->IsInitialized()) && (this->GetMTime() <= m_TimeOfHeaderInitialization.GetMTime())) + return; + + itkDebugMacro(<< "GenerateOutputInformation()"); + + output->Initialize(input); + output->GetGeometry()->SetSpacing(input->GetGeometry()->GetSpacing()); + output->GetGeometry()->Modified(); + output->SetPropertyList(input->GetPropertyList()->Clone()); + + m_TimeOfHeaderInitialization.Modified(); +} + +void mitk::PhotoacousticBModeFilter::GenerateData() +{ + GenerateOutputInformation(); + mitk::Image::Pointer input = this->GetInput(); + mitk::Image::Pointer output = this->GetOutput(); + + if (!output->IsInitialized()) + return; + + mitk::ImageReadAccessor reader(input); + + unsigned int size = output->GetDimension(0) * output->GetDimension(1) * output->GetDimension(2); + + float* InputData = (float*)const_cast(reader.GetData()); + float* OutputData = new float[size]; + if(!m_UseLogFilter) + for (unsigned int i = 0; i < size; ++i) + { + OutputData[i] = abs(InputData[i]); + } + else + { + for (unsigned int i = 0; i < size; ++i) + { + OutputData[i] = log(abs(InputData[i])); + } + } + + output->SetImportVolume(OutputData, 0, 0, mitk::Image::ImportMemoryManagementType::ManageMemory); + + m_TimeOfHeaderInitialization.Modified(); +} \ No newline at end of file diff --git a/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.cpp b/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.cpp new file mode 100644 index 0000000000..575c29b240 --- /dev/null +++ b/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.cpp @@ -0,0 +1,264 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ + +#if defined(PHOTOACOUSTICS_USE_GPU) || DOXYGEN + +#include "./OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.h" +#include "usServiceReference.h" + +mitk::PhotoacousticOCLBeamformingFilter::PhotoacousticOCLBeamformingFilter() +: m_PixelCalculation( NULL ), m_InputImage(mitk::Image::New()), m_ApodizationBuffer(nullptr), m_MemoryLocationsBuffer(nullptr), m_DelaysBuffer(nullptr), m_UsedLinesBuffer(nullptr) +{ + this->AddSourceFile("DAS.cl"); + this->AddSourceFile("DMAS.cl"); + this->AddSourceFile("sDMAS.cl"); + this->m_FilterID = "OpenCLBeamformingFilter"; + + this->Initialize(); + + unsigned int dim[] = { 128, 2048, 2 }; + + mitk::Vector3D spacing; + spacing[0] = 1; + spacing[1] = 1; + spacing[2] = 1; + + m_InputImage->Initialize(mitk::MakeScalarPixelType(), 3, dim); + m_InputImage->SetSpacing(spacing); + + m_ChunkSize[0] = 128; + m_ChunkSize[1] = 128; + m_ChunkSize[2] = 8; + + m_UsedLinesCalculation = mitk::OCLUsedLinesCalculation::New(); + m_DelayCalculation = mitk::OCLDelayCalculation::New(); +} + +mitk::PhotoacousticOCLBeamformingFilter::~PhotoacousticOCLBeamformingFilter() +{ + if ( this->m_PixelCalculation ) + { + clReleaseKernel( m_PixelCalculation ); + } + + if (m_ApodizationBuffer) clReleaseMemObject(m_ApodizationBuffer); +} + +void mitk::PhotoacousticOCLBeamformingFilter::Update() +{ + //Check if context & program available + if (!this->Initialize()) + { + us::ServiceReference ref = GetModuleContext()->GetServiceReference(); + OclResourceService* resources = GetModuleContext()->GetService(ref); + + // clean-up also the resources + resources->InvalidateStorage(); + mitkThrow() <<"Filter is not initialized. Cannot update."; + } + else{ + // Execute + this->Execute(); + } +} + +void mitk::PhotoacousticOCLBeamformingFilter::UpdateDataBuffers() +{ + /*us::ServiceReference ref = GetModuleContext()->GetServiceReference(); + OclResourceService* resources = GetModuleContext()->GetService(ref); + cl_ulong globalMemSize = oclGetGlobalMemSize(resources->GetCurrentDevice());*/ + //Initialize the Output + + try + { + MITK_DEBUG << "Updating Workgroup size for new dimensions"; + size_t outputSize = (size_t)m_Conf.ReconstructionLines * (size_t)m_Conf.SamplesPerLine * (size_t)m_Conf.inputDim[2]; + m_OutputDim[0] = m_Conf.ReconstructionLines; + m_OutputDim[1] = m_Conf.SamplesPerLine; + m_OutputDim[2] = m_Conf.inputDim[2]; + this->InitExec(this->m_PixelCalculation, m_OutputDim, outputSize, sizeof(float)); + } + catch (const mitk::Exception& e) + { + MITK_ERROR << "Caught exception while initializing filter: " << e.what(); + return; + } + + if (BeamformingSettings::SettingsChangedOpenCL(m_Conf, m_ConfOld)) + { + cl_int clErr = 0; + MITK_DEBUG << "Updating GPU Buffers for new configuration"; + + // create the apodisation buffer + + if (m_Apodisation == nullptr) + { + MITK_INFO << "No apodisation function set; Beamforming will be done without any apodisation."; + m_Apodisation = new float[1]; + m_Apodisation[0] = 1; + m_ApodArraySize = 1; + } + + us::ServiceReference ref = GetModuleContext()->GetServiceReference(); + OclResourceService* resources = GetModuleContext()->GetService(ref); + cl_context gpuContext = resources->GetContext(); + + if (m_ApodizationBuffer) clReleaseMemObject(m_ApodizationBuffer); + + this->m_ApodizationBuffer = clCreateBuffer(gpuContext, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR, sizeof(float) * m_ApodArraySize, m_Apodisation, &clErr); + CHECK_OCL_ERR(clErr); + + // calculate used lines + + m_UsedLinesCalculation->SetConfig(m_Conf); + m_UsedLinesCalculation->Update(); + m_UsedLinesBuffer = m_UsedLinesCalculation->GetGPUOutput()->GetGPUBuffer(); + + // calculate the Delays + m_DelayCalculation->SetConfig(m_Conf); + m_DelayCalculation->SetInputs(m_UsedLinesBuffer); + m_DelayCalculation->Update(); + + m_DelaysBuffer = m_DelayCalculation->GetGPUOutput()->GetGPUBuffer(); + + m_ConfOld = m_Conf; + } +} + +void mitk::PhotoacousticOCLBeamformingFilter::Execute() +{ + cl_int clErr = 0; + UpdateDataBuffers(); + + clErr = clSetKernelArg(this->m_PixelCalculation, 2, sizeof(cl_mem), &(this->m_UsedLinesBuffer)); + clErr |= clSetKernelArg(this->m_PixelCalculation, 3, sizeof(cl_mem), &(this->m_DelaysBuffer)); + clErr |= clSetKernelArg(this->m_PixelCalculation, 4, sizeof(cl_mem), &(this->m_ApodizationBuffer)); + clErr |= clSetKernelArg(this->m_PixelCalculation, 5, sizeof(cl_ushort), &(this->m_ApodArraySize)); + clErr |= clSetKernelArg(this->m_PixelCalculation, 6, sizeof(cl_uint), &(this->m_Conf.inputDim[0])); + clErr |= clSetKernelArg(this->m_PixelCalculation, 7, sizeof(cl_uint), &(this->m_Conf.inputDim[1])); + clErr |= clSetKernelArg(this->m_PixelCalculation, 8, sizeof(cl_uint), &(this->m_Conf.inputDim[2])); + clErr |= clSetKernelArg(this->m_PixelCalculation, 9, sizeof(cl_uint), &(this->m_Conf.ReconstructionLines)); + clErr |= clSetKernelArg(this->m_PixelCalculation, 10, sizeof(cl_uint), &(this->m_Conf.SamplesPerLine)); + + // execute the filter on a 3D NDRange + if (m_OutputDim[2] == 1 || m_ChunkSize[2] == 1) + { + if(!this->ExecuteKernelChunksInBatches(m_PixelCalculation, 2, m_ChunkSize, 16, 50)) + mitkThrow() << "openCL Error when executing Kernel"; + } + else + { + if(!this->ExecuteKernelChunksInBatches(m_PixelCalculation, 3, m_ChunkSize, 16, 50)) + mitkThrow() << "openCL Error when executing Kernel"; + } + + // signalize the GPU-side data changed + m_Output->Modified( GPU_DATA ); +} + +us::Module *mitk::PhotoacousticOCLBeamformingFilter::GetModule() +{ + return us::GetModuleContext()->GetModule(); +} + +bool mitk::PhotoacousticOCLBeamformingFilter::Initialize() +{ + bool buildErr = true; + cl_int clErr = 0; + + if ( OclFilter::Initialize() ) + { + switch (m_Conf.Algorithm) + { + case BeamformingSettings::BeamformingAlgorithm::DAS: + { + this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckDAS", &clErr); + break; + } + case BeamformingSettings::BeamformingAlgorithm::DMAS: + { + this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckDMAS", &clErr); + break; + } + case BeamformingSettings::BeamformingAlgorithm::sDMAS: + { + this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "cksDMAS", &clErr); + break; + } + default: + { + MITK_INFO << "No beamforming algorithm specified, setting to DAS"; + this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckDAS", &clErr); + break; + } + } + buildErr |= CHECK_OCL_ERR( clErr ); + } + + CHECK_OCL_ERR(clErr); + + return (OclFilter::IsInitialized() && buildErr ); +} + +void mitk::PhotoacousticOCLBeamformingFilter::SetInput(mitk::Image::Pointer image) +{ + OclDataSetToDataSetFilter::SetInput(image); + + m_InputImage = image; + m_Conf.inputDim[0] = m_InputImage->GetDimension(0); + m_Conf.inputDim[1] = m_InputImage->GetDimension(1); + m_Conf.inputDim[2] = m_InputImage->GetDimension(2); +} + +void mitk::PhotoacousticOCLBeamformingFilter::SetInput(void* data, unsigned int* dimensions, unsigned int BpE) +{ + OclDataSetToDataSetFilter::SetInput(data, dimensions[0] * dimensions[1] * dimensions[2], BpE); + + m_Conf.inputDim[0] = dimensions[0]; + m_Conf.inputDim[1] = dimensions[1]; + m_Conf.inputDim[2] = dimensions[2]; +} + +mitk::Image::Pointer mitk::PhotoacousticOCLBeamformingFilter::GetOutputAsImage() +{ + mitk::Image::Pointer outputImage = mitk::Image::New(); + + if (m_Output->IsModified(GPU_DATA)) + { + void* pData = m_Output->TransferDataToCPU(m_CommandQue); + + const unsigned int dimension = 3; + unsigned int dimensions[3] = { (unsigned int)m_OutputDim[0], (unsigned int)m_OutputDim[1], (unsigned int)m_OutputDim[2] }; + + const mitk::SlicedGeometry3D::Pointer p_slg = m_InputImage->GetSlicedGeometry(); + + MITK_DEBUG << "Creating new MITK Image."; + + outputImage->Initialize(this->GetOutputType(), dimension, dimensions); + outputImage->SetSpacing(p_slg->GetSpacing()); + outputImage->SetImportVolume(pData, 0, 0, mitk::Image::ImportMemoryManagementType::ManageMemory); + } + + MITK_DEBUG << "Image Initialized."; + + return outputImage; +} + +void* mitk::PhotoacousticOCLBeamformingFilter::GetOutput() +{ + return OclDataSetToDataSetFilter::GetOutput(); +} +#endif diff --git a/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLDelayCalculation.cpp b/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLDelayCalculation.cpp new file mode 100644 index 0000000000..bbee18bc42 --- /dev/null +++ b/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLDelayCalculation.cpp @@ -0,0 +1,125 @@ +/*=================================================================== + +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() + : m_PixelCalculation(NULL) +{ + 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.ReconstructionLines / 2, m_Conf.SamplesPerLine, 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.DelayCalculationMethod == BeamformingSettings::DelayCalc::QuadApprox) + m_DelayMultiplicatorRaw = pow(1 / (m_Conf.TimeSpacing*m_Conf.SpeedOfSound) * m_Conf.Pitch * (float)m_Conf.TransducerElements / (float)m_Conf.inputDim[0], 2) / 2; + else if (m_Conf.DelayCalculationMethod == BeamformingSettings::DelayCalc::Spherical) + m_DelayMultiplicatorRaw = 1 / (m_Conf.TimeSpacing*m_Conf.SpeedOfSound) * (m_Conf.Pitch*(float)m_Conf.TransducerElements); + + // as openCL does not support bool as a kernel argument, we need to buffer this value in a char... + m_IsPAImage = m_Conf.isPhotoacousticImage; + + clErr = clSetKernelArg(this->m_PixelCalculation, 1, sizeof(cl_mem), &(this->m_UsedLines)); + clErr |= clSetKernelArg(this->m_PixelCalculation, 2, sizeof(cl_uint), &(this->m_Conf.inputDim[0])); + clErr |= clSetKernelArg(this->m_PixelCalculation, 3, sizeof(cl_uint), &(this->m_Conf.inputDim[1])); + clErr |= clSetKernelArg(this->m_PixelCalculation, 4, sizeof(cl_uint), &(this->m_Conf.ReconstructionLines)); + clErr |= clSetKernelArg(this->m_PixelCalculation, 5, sizeof(cl_uint), &(this->m_Conf.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.DelayCalculationMethod == BeamformingSettings::DelayCalc::QuadApprox) + this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckDelayCalculationQuad", &clErr); + if (m_Conf.DelayCalculationMethod == BeamformingSettings::DelayCalc::Spherical) + this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckDelayCalculationSphe", &clErr); + buildErr |= CHECK_OCL_ERR(clErr); + } + return (OclFilter::IsInitialized() && buildErr); +} \ No newline at end of file diff --git a/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLUsedLinesCalculation.cpp b/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLUsedLinesCalculation.cpp new file mode 100644 index 0000000000..c44b1a98d7 --- /dev/null +++ b/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLUsedLinesCalculation.cpp @@ -0,0 +1,116 @@ +/*=================================================================== + +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 +#define _USE_MATH_DEFINES + +#include +#include "./OpenCLFilter/mitkPhotoacousticOCLUsedLinesCalculation.h" +#include "usServiceReference.h" +#include "mitkImageReadAccessor.h" + +mitk::OCLUsedLinesCalculation::OCLUsedLinesCalculation() + : m_PixelCalculation(NULL) +{ + 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.ReconstructionLines, m_Conf.SamplesPerLine, 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.Angle / 360 * 2 * M_PI) * ((m_Conf.SpeedOfSound * m_Conf.TimeSpacing)) / (m_Conf.Pitch * m_Conf.TransducerElements)) * m_Conf.inputDim[0]; + + clErr = clSetKernelArg(this->m_PixelCalculation, 1, sizeof(cl_float), &(this->m_part)); + clErr |= clSetKernelArg(this->m_PixelCalculation, 2, sizeof(cl_uint), &(this->m_Conf.inputDim[0])); + clErr |= clSetKernelArg(this->m_PixelCalculation, 3, sizeof(cl_uint), &(this->m_Conf.inputDim[1])); + clErr |= clSetKernelArg(this->m_PixelCalculation, 4, sizeof(cl_uint), &(this->m_Conf.ReconstructionLines)); + clErr |= clSetKernelArg(this->m_PixelCalculation, 5, sizeof(cl_uint), &(this->m_Conf.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/mitkPhotoacousticBeamformingFilter.cpp new file mode 100644 index 0000000000..9fff61a04e --- /dev/null +++ b/Modules/PhotoacousticsAlgorithms/source/mitkPhotoacousticBeamformingFilter.cpp @@ -0,0 +1,803 @@ +/*=================================================================== +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. + +===================================================================*/ + +#define _USE_MATH_DEFINES + +#include "mitkProperties.h" +#include "mitkImageReadAccessor.h" +#include +#include +#include +#include +#include +#include +#include "mitkImageCast.h" +#include "mitkPhotoacousticBeamformingFilter.h" + +mitk::BeamformingFilter::BeamformingFilter() : m_OutputData(nullptr), m_InputData(nullptr), m_Message("noMessage") +{ + this->SetNumberOfIndexedInputs(1); + this->SetNumberOfRequiredInputs(1); + + m_ProgressHandle = [](int, std::string) {}; + + m_BeamformingOclFilter = mitk::PhotoacousticOCLBeamformingFilter::New(); + + m_VonHannFunction = VonHannFunction(m_Conf.apodizationArraySize); + m_HammFunction = HammFunction(m_Conf.apodizationArraySize); + m_BoxFunction = BoxFunction(m_Conf.apodizationArraySize); +} + +void mitk::BeamformingFilter::SetProgressHandle(std::function progressHandle) +{ + m_ProgressHandle = progressHandle; +} + +mitk::BeamformingFilter::~BeamformingFilter() +{ + delete[] m_VonHannFunction; + delete[] m_HammFunction; + delete[] m_BoxFunction; +} + +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.ReconstructionLines, m_Conf.SamplesPerLine, input->GetDimension(2) }; + output->Initialize(mitk::MakeScalarPixelType(), 3, dim); + + mitk::Vector3D spacing; + spacing[0] = m_Conf.Pitch * m_Conf.TransducerElements * 1000 / m_Conf.ReconstructionLines; + spacing[1] = (m_Conf.TimeSpacing * m_Conf.inputDim[1]) / 2 * m_Conf.SpeedOfSound * 1000 / m_Conf.SamplesPerLine; + 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(); + mitk::Image::Pointer output = this->GetOutput(); + + if (!output->IsInitialized()) + return; + + float* ApodWindow; + if (m_ConfOld.apodizationArraySize != m_Conf.apodizationArraySize) + { + delete[] m_VonHannFunction; + delete[] m_HammFunction; + delete[] m_BoxFunction; + m_VonHannFunction = VonHannFunction(m_Conf.apodizationArraySize); + m_HammFunction = HammFunction(m_Conf.apodizationArraySize); + m_BoxFunction = BoxFunction(m_Conf.apodizationArraySize); + + m_ConfOld = m_Conf; + } + + // set the appropiate apodization window + switch (m_Conf.Apod) + { + case BeamformingSettings::Apodization::Hann: + ApodWindow = m_VonHannFunction; + break; + case BeamformingSettings::Apodization::Hamm: + ApodWindow = m_HammFunction; + break; + case BeamformingSettings::Apodization::Box: + ApodWindow = m_BoxFunction; + break; + default: + ApodWindow = m_BoxFunction; + break; + } + + auto begin = std::chrono::high_resolution_clock::now(); // debbuging the performance... + + if (!m_Conf.UseGPU) + { + 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_OutputData = new float[m_Conf.ReconstructionLines*m_Conf.SamplesPerLine]; + + // 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.Algorithm == BeamformingSettings::BeamformingAlgorithm::DAS) + { + if (m_Conf.DelayCalculationMethod == BeamformingSettings::DelayCalc::QuadApprox) + { + for (short line = 0; line < outputDim[0]; ++line) + { + threads[line] = std::thread(&BeamformingFilter::DASQuadraticLine, this, m_InputData, m_OutputData, inputDim, outputDim, line, ApodWindow, m_Conf.apodizationArraySize); + } + } + else if (m_Conf.DelayCalculationMethod == BeamformingSettings::DelayCalc::Spherical) + { + for (short line = 0; line < outputDim[0]; ++line) + { + threads[line] = std::thread(&BeamformingFilter::DASSphericalLine, this, m_InputData, m_OutputData, inputDim, outputDim, line, ApodWindow, m_Conf.apodizationArraySize); + } + } + } + else if (m_Conf.Algorithm == BeamformingSettings::BeamformingAlgorithm::DMAS) + { + if (m_Conf.DelayCalculationMethod == BeamformingSettings::DelayCalc::QuadApprox) + { + for (short line = 0; line < outputDim[0]; ++line) + { + threads[line] = std::thread(&BeamformingFilter::DMASQuadraticLine, this, m_InputData, m_OutputData, inputDim, outputDim, line, ApodWindow, m_Conf.apodizationArraySize); + } + } + else if (m_Conf.DelayCalculationMethod == BeamformingSettings::DelayCalc::Spherical) + { + for (short line = 0; line < outputDim[0]; ++line) + { + threads[line] = std::thread(&BeamformingFilter::DMASSphericalLine, this, m_InputData, m_OutputData, inputDim, outputDim, line, ApodWindow, m_Conf.apodizationArraySize); + } + } + } + else if (m_Conf.Algorithm == BeamformingSettings::BeamformingAlgorithm::sDMAS) + { + if (m_Conf.DelayCalculationMethod == BeamformingSettings::DelayCalc::QuadApprox) + { + for (short line = 0; line < outputDim[0]; ++line) + { + threads[line] = std::thread(&BeamformingFilter::sDMASQuadraticLine, this, m_InputData, m_OutputData, inputDim, outputDim, line, ApodWindow, m_Conf.apodizationArraySize); + } + } + else if (m_Conf.DelayCalculationMethod == BeamformingSettings::DelayCalc::Spherical) + { + for (short line = 0; line < outputDim[0]; ++line) + { + threads[line] = std::thread(&BeamformingFilter::sDMASSphericalLine, this, m_InputData, m_OutputData, inputDim, outputDim, line, ApodWindow, m_Conf.apodizationArraySize); + } + } + } + // 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; + } + + 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; + (long)(batchDim[0] * batchDim[1]) * 4 + // Input image (float) + (long)(m_Conf.ReconstructionLines * m_Conf.SamplesPerLine) * 4 // Output image (float) + > availableMemory - + (long)(m_Conf.ReconstructionLines / 2 * m_Conf.SamplesPerLine) * 2 - // Delays buffer (unsigned short) + (long)(m_Conf.ReconstructionLines * m_Conf.SamplesPerLine) * 3 * 2 - // UsedLines buffer (unsigned short) + 100 * 1024; // 100 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.inputDim[2] = batchDimLast[2]; + } + else + { + inputBatch->Initialize(mitk::MakeScalarPixelType(), 3, batchDim); + m_Conf.inputDim[2] = batchDim[2]; + } + + inputBatch->SetSpacing(input->GetGeometry()->GetSpacing()); + + inputBatch->SetImportVolume(&(((float*)copy.GetData())[input->GetDimension(0) * input->GetDimension(1) * batchSize * i])); + + m_BeamformingOclFilter->SetApodisation(ApodWindow, m_Conf.apodizationArraySize); + m_BeamformingOclFilter->SetConfig(m_Conf); + m_BeamformingOclFilter->SetInput(inputBatch); + m_BeamformingOclFilter->Update(); + + void* out = m_BeamformingOclFilter->GetOutput(); + + for(unsigned int slice = 0; slice < m_Conf.inputDim[2]; ++slice) + { + output->SetImportSlice( + &(((float*)out)[m_Conf.ReconstructionLines * m_Conf.SamplesPerLine * 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.ReconstructionLines * m_Conf.SamplesPerLine * m_Conf.inputDim[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; +} + +float* mitk::BeamformingFilter::VonHannFunction(int samples) +{ + float* ApodWindow = new float[samples]; + + for (int n = 0; n < samples; ++n) + { + ApodWindow[n] = (1 - cos(2 * M_PI * n / (samples - 1))) / 2; + } + + return ApodWindow; +} + +float* mitk::BeamformingFilter::HammFunction(int samples) +{ + float* ApodWindow = new float[samples]; + + for (int n = 0; n < samples; ++n) + { + ApodWindow[n] = 0.54 - 0.46*cos(2 * M_PI*n / (samples - 1)); + } + + return ApodWindow; +} + +float* mitk::BeamformingFilter::BoxFunction(int samples) +{ + float* ApodWindow = new float[samples]; + + for (int n = 0; n < samples; ++n) + { + ApodWindow[n] = 1; + } + + return ApodWindow; +} + +void mitk::BeamformingFilter::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 * M_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::BeamformingFilter::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 * M_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::BeamformingFilter::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 * M_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::BeamformingFilter::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 * M_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::BeamformingFilter::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 * M_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::BeamformingFilter::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 * M_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/mitkPhotoacousticImage.cpp b/Modules/PhotoacousticsAlgorithms/source/mitkPhotoacousticImage.cpp similarity index 72% copy from Modules/PhotoacousticsAlgorithms/mitkPhotoacousticImage.cpp copy to Modules/PhotoacousticsAlgorithms/source/mitkPhotoacousticImage.cpp index 9ba451e9cd..c74336ba67 100644 --- a/Modules/PhotoacousticsAlgorithms/mitkPhotoacousticImage.cpp +++ b/Modules/PhotoacousticsAlgorithms/source/mitkPhotoacousticImage.cpp @@ -1,641 +1,541 @@ /*=================================================================== 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 "mitkPhotoacousticImage.h" -#include "itkBModeImageFilter.h" -#include "itkPhotoacousticBModeImageFilter.h" +#include "../ITKFilter/ITKUltrasound/itkBModeImageFilter.h" +#include "../ITKFilter/itkPhotoacousticBModeImageFilter.h" #include "mitkImageCast.h" #include "mitkITKImageImport.h" #include "mitkPhotoacousticBeamformingFilter.h" #include #include -#include +#include "./OpenCLFilter/mitkPhotoacousticBModeFilter.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 "itkFFT1DComplexConjugateToRealImageFilter.h" -#include "itkFFT1DRealToComplexConjugateImageFilter.h" +#include "../ITKFilter/ITKUltrasound/itkFFT1DComplexConjugateToRealImageFilter.h" +#include "../ITKFilter/ITKUltrasound/itkFFT1DRealToComplexConjugateImageFilter.h" -mitk::PhotoacousticImage::PhotoacousticImage() +mitk::PhotoacousticImage::PhotoacousticImage() : m_BeamformingFilter(BeamformingFilter::New()) { MITK_INFO << "[PhotoacousticImage Debug] created that image"; } mitk::PhotoacousticImage::~PhotoacousticImage() { MITK_INFO << "[PhotoacousticImage Debug] destroyed that image"; } -mitk::Image::Pointer mitk::PhotoacousticImage::ApplyBmodeFilter(mitk::Image::Pointer inputImage, BModeMethod method, bool UseLogFilter, float resampleSpacing) +mitk::Image::Pointer mitk::PhotoacousticImage::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) { - auto input = ApplyCropping(inputImage, 0, 0, 0, 0, 0, inputImage->GetDimension(2) - 1); - PhotoacousticBModeFilter::Pointer filter = PhotoacousticBModeFilter::New(); - filter->SetParameters(UseLogFilter); - filter->SetInput(input); - filter->Update(); + 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(); - auto out = filter->GetOutput(); + out = filter->GetOutput(); - if(resampleSpacing == 0) - return out; + 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::ShapeDetection) + 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::PhotoacousticImage::ApplyScatteringCompensation(mitk::Image::Pointer inputImage, int scattering) { typedef itk::Image< float, 3 > itkFloatImageType; typedef itk::MultiplyImageFilter MultiplyImageFilterType; itkFloatImageType::Pointer itkImage; mitk::CastToItkImage(inputImage, itkImage); MultiplyImageFilterType::Pointer multiplyFilter = MultiplyImageFilterType::New(); multiplyFilter->SetInput1(itkImage); multiplyFilter->SetInput2(m_FluenceCompResizedItk.at(m_ScatteringCoefficient)); return mitk::GrabItkImageMemory(multiplyFilter->GetOutput()); }*/ mitk::Image::Pointer mitk::PhotoacousticImage::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::PhotoacousticImage::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 those float, short, float are used at all... though it's easy to add other ones + // 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 unsigned shorto the cropped image + // 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 unsigned shorto the cropped image + // 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::ReferenceMemory); return output; } -mitk::Image::Pointer mitk::PhotoacousticImage::ApplyBeamforming(mitk::Image::Pointer inputImage, BeamformingFilter::beamformingSettings config, int cutoff, std::function progressHandle) +mitk::Image::Pointer mitk::PhotoacousticImage::ApplyBeamforming(mitk::Image::Pointer inputImage, BeamformingSettings config, std::string& message, std::function progressHandle) { - // crop the image - // set the Maximum Size of the image to 4096 - unsigned short lowerCutoff = 0; - if (((unsigned int)(4096 + cutoff)) < inputImage->GetDimension(1)) + Image::Pointer processedImage = inputImage; + if (inputImage->GetDimension() != 3) { - lowerCutoff = (unsigned short)(inputImage->GetDimension(1) - 4096); + processedImage->Initialize(mitk::MakeScalarPixelType(), 3, inputImage->GetDimensions()); + processedImage->SetSpacing(inputImage->GetGeometry()->GetSpacing()); + + mitk::ImageReadAccessor copy(inputImage); + + processedImage->SetImportVolume(copy.GetData()); } - config.RecordTime = config.RecordTime - (cutoff + lowerCutoff) / inputImage->GetDimension(1) * config.RecordTime; // adjust the recorded time lost by cropping - progressHandle(0, "cropping image"); + config.RecordTime = config.RecordTime - (float)(config.upperCutoff) / (float)inputImage->GetDimension(1) * config.RecordTime; // adjust the recorded time lost by cropping + progressHandle(0, "converting image"); if (!config.partial) { config.CropBounds[0] = 0; config.CropBounds[1] = inputImage->GetDimension(2) - 1; } + processedImage = ApplyCropping(inputImage, config.upperCutoff, 0, 0, 0, config.CropBounds[0], config.CropBounds[1]); - Image::Pointer processedImage = ApplyCropping(inputImage, cutoff, lowerCutoff, 0, 0, config.CropBounds[0], config.CropBounds[1]); - - // resample the image in horizontal direction - if (inputImage->GetDimension(0) != config.ReconstructionLines) - { - progressHandle(0, "resampling image"); - auto begin = std::chrono::high_resolution_clock::now(); - unsigned int dim[2] = { config.ReconstructionLines, processedImage->GetDimension(1) }; - processedImage = ApplyResampling(processedImage, dim); - auto end = std::chrono::high_resolution_clock::now(); - MITK_DEBUG << "Upsampling from " << inputImage->GetDimension(0) << " to " << config.ReconstructionLines << " lines completed in " << ((double)std::chrono::duration_cast(end - begin).count()) / 1000000 << "ms" << std::endl; - } + config.inputDim[0] = processedImage->GetDimension(0); + config.inputDim[1] = processedImage->GetDimension(1); + config.inputDim[2] = processedImage->GetDimension(2); // perform the beamforming - BeamformingFilter::Pointer Beamformer = BeamformingFilter::New(); - Beamformer->SetInput(processedImage); - Beamformer->Configure(config); - Beamformer->SetProgressHandle(progressHandle); - Beamformer->UpdateLargestPossibleRegion(); + m_BeamformingFilter->SetInput(processedImage); + m_BeamformingFilter->Configure(config); + m_BeamformingFilter->SetProgressHandle(progressHandle); + m_BeamformingFilter->UpdateLargestPossibleRegion(); - processedImage = Beamformer->GetOutput(); + processedImage = m_BeamformingFilter->GetOutput(); + message = m_BeamformingFilter->GetMessageString(); return processedImage; } mitk::Image::Pointer mitk::PhotoacousticImage::BandpassFilter(mitk::Image::Pointer data, float recordTime, float BPHighPass, float BPLowPass, float alpha) { 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, alpha); 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::PhotoacousticImage::BPFunction(mitk::Image::Pointer reference, int cutoffFrequencyPixelHighPass, int cutoffFrequencyPixelLowPass, float alpha) { float* imageData = new float[reference->GetDimension(0)*reference->GetDimension(1)]; // tukey window float width = reference->GetDimension(1) / 2 - (float)cutoffFrequencyPixelHighPass - (float)cutoffFrequencyPixelLowPass; float center = (float)cutoffFrequencyPixelHighPass / 2 + width / 2; MITK_INFO << width << "width " << center << "center " << alpha; for (unsigned int n = 0; n < reference->GetDimension(1); ++n) { imageData[reference->GetDimension(0)*n] = 0; } - - for (int n = 0; n < width; ++n) + if (alpha < 0.00001) { - if (n <= (alpha*(width - 1)) / 2) - { - imageData[reference->GetDimension(0)*(int)(n + center - (width / 2))] = (1 + cos(M_PI*(2 * n / (alpha*(width - 1)) - 1))) / 2; - } - else if (n >= (width - 1)*(1 - alpha / 2) && n <= (width - 1)) + for (int n = 0; n < width; ++n) { - imageData[reference->GetDimension(0)*(int)(n + center - (width / 2))] = (1 + cos(M_PI*(2 * n / (alpha*(width - 1)) + 1 - 2 / alpha))) / 2; + if (n <= (alpha*(width - 1)) / 2) + { + imageData[reference->GetDimension(0)*(int)(n + center - (width / 2))] = (1 + cos(M_PI*(2 * n / (alpha*(width - 1)) - 1))) / 2; + } + else if (n >= (width - 1)*(1 - alpha / 2)) + { + imageData[reference->GetDimension(0)*(int)(n + center - (width / 2))] = (1 + cos(M_PI*(2 * n / (alpha*(width - 1)) + 1 - 2 / alpha))) / 2; + } + else + { + imageData[reference->GetDimension(0)*(int)(n + center - (width / 2))] = 1; + } } - else + } + else + { + for (int n = 0; n < width; ++n) { imageData[reference->GetDimension(0)*(int)(n + center - (width / 2))] = 1; } } - // Butterworth-Filter /* // first, write the HighPass if (cutoffFrequencyPixelHighPass != reference->GetDimension(1) / 2) { for (int n = 0; n < reference->GetDimension(1) / 2; ++n) { imageData[reference->GetDimension(0)*n] = 1 / (1 + pow( (float)n / (float)(reference->GetDimension(1) / 2 - cutoffFrequencyPixelHighPass) , 2 * butterworthOrder)); } } else { for (int n = 0; n < reference->GetDimension(1) / 2; ++n) { imageData[reference->GetDimension(0)*n] = 1; } } // now, the LowPass for (int n = 0; n < reference->GetDimension(1) / 2; ++n) { imageData[reference->GetDimension(0)*n] *= 1 / (1 + pow( (float)(reference->GetDimension(1) / 2 - 1 - n) / (float)(reference->GetDimension(1) / 2 - cutoffFrequencyPixelLowPass) , 2 * butterworthOrder)); } */ // 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 (ImageType::IndexValueType slice = 0; slice < reference->GetDimension(2); ++slice) { for (ImageType::IndexValueType line = 0; line < reference->GetDimension(0); ++line) { for (ImageType::IndexValueType 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; } - - -/* -mitk::CropFilter::CropFilter() - : m_PixelCalculation(NULL) -{ - this->AddSourceFile("CropFilter.cl"); - - this->m_FilterID = "CropFilter"; -} - -mitk::CropFilter::~CropFilter() -{ - if (this->m_PixelCalculation) - { - clReleaseKernel(m_PixelCalculation); - } -} - -void mitk::CropFilter::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::CropFilter::Execute() -{ - cl_int clErr = 0; - - try - { - this->InitExec(this->m_PixelCalculation); - } - catch (const mitk::Exception& e) - { - MITK_ERROR << "Catched exception while initializing filter: " << e.what(); - return; - } - - us::ServiceReference ref = GetModuleContext()->GetServiceReference(); - OclResourceService* resources = GetModuleContext()->GetService(ref); - cl_context gpuContext = resources->GetContext(); - - unsigned int size = m_OutputDim[0] * m_OutputDim[1] * m_OutputDim[2] * m_Images; - - cl_mem cl_input = clCreateBuffer(gpuContext, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR, sizeof(float) * size, m_Data, &clErr); - CHECK_OCL_ERR(clErr); - - // set kernel arguments - clErr = clSetKernelArg(this->m_PixelCalculation, 2, sizeof(cl_mem), &cl_input); - clErr |= clSetKernelArg(this->m_PixelCalculation, 3, sizeof(cl_ushort), &(this->m_Images)); - - CHECK_OCL_ERR(clErr); - - // execute the filter on a 3D NDRange - this->ExecuteKernel(m_PixelCalculation, 3); - - // signalize the GPU-side data changed - m_Output->Modified(GPU_DATA); -} - -us::Module *mitk::CropFilter::GetModule() -{ - return us::GetModuleContext()->GetModule(); -} - -bool mitk::CropFilter::Initialize() -{ - bool buildErr = true; - cl_int clErr = 0; - - if (OclFilter::Initialize()) - { - this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckCrop", &clErr); - buildErr |= CHECK_OCL_ERR(clErr); - } - return (OclFilter::IsInitialized() && buildErr); -} - -void mitk::CropFilter::SetInput(mitk::Image::Pointer image) -{ - if (image->GetDimension() != 3) - { - mitkThrowException(mitk::Exception) << "Input for " << this->GetNameOfClass() << - " is not 3D. The filter only supports 3D. Please change your input."; - } - OclImageToImageFilter::SetInput(image); -} - -mitk::Image::Pointer mitk::CropFilter::GetOutput() -{ - if (m_Output->IsModified(GPU_DATA)) - { - void* pData = m_Output->TransferDataToCPU(m_CommandQue); - - const unsigned int dimension = 3; - unsigned int* dimensions = m_OutputDim; - - const mitk::SlicedGeometry3D::Pointer p_slg = m_Input->GetMITKImage()->GetSlicedGeometry(); - - MITK_DEBUG << "Creating new MITK Image."; - - m_Output->GetMITKImage()->Initialize(this->GetOutputType(), dimension, dimensions); - m_Output->GetMITKImage()->SetSpacing(p_slg->GetSpacing()); - m_Output->GetMITKImage()->SetGeometry(m_Input->GetMITKImage()->GetGeometry()); - m_Output->GetMITKImage()->SetImportVolume(pData, 0, 0, mitk::Image::ReferenceMemory); - } - - MITK_DEBUG << "Image Initialized."; - - return m_Output->GetMITKImage(); -} - -*/ diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/CMakeLists.txt b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/CMakeLists.txt index ce750d05d7..0b44d554e6 100644 --- a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/CMakeLists.txt @@ -1,7 +1,11 @@ project(org_mitk_gui_qt_photoacoustics_imageprocessing) mitk_create_plugin( EXPORT_DIRECTIVE IMAGEPROCESSING_EXPORT EXPORTED_INCLUDE_SUFFIXES src MODULE_DEPENDS MitkQtWidgetsExt MitkPhotoacousticsAlgorithms ) + +IF(MITK_USE_OpenCL) + add_definitions(-DPHOTOACOUSTICS_USE_GPU) +ENDIF(MITK_USE_OpenCL) \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/Manual.dox index d96263f413..0aea28cd07 100644 --- a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/Manual.dox @@ -1,17 +1,62 @@ /** -\page org_mitk_gui_qt_photoacoustics_imageprocessing The Imageprocessing +\page org_mitk_gui_qt_photoacoustics_imageprocessing The Photoacoustics Imageprocessing Plugin -\imageMacro{icon.png,"Icon of Imageprocessing",2.00} +\imageMacro{pai.png,"Icon of Imageprocessing",2.00} \tableofcontents \section org_mitk_gui_qt_photoacoustics_imageprocessingOverview Overview -Describe the features of your awesome plugin here +This plugin offers an interface to perform image processing on photoacoustic, as well as ultrasound images, i.e. to use beamforming and post-processing filters. +For convenience, image processing can be done automatically for a whole batch of files containing PA or US data. + +\section org_mitk_gui_qt_photoacoustics_imageprocessingPrerequisites Prerequisites +To use the much more performant openCL filters which run on the graphics card, MITK has to be able to use openCL, for which it is necessary to install the openCL implementation provided by your graphics card vendor. + +\section org_mitk_gui_qt_photoacoustics_imageprocessingFiltering Using the filters +To perform image processing, simply load an image into MITK and select it in the Data manager. Only the selected image will be processed by the filters. +\imageMacro{QmikPhotoacousticsImageProcessing_DataManager.png,"Select the image to be processed",7.62} +Before performing reconstruction or using other filters those can be configured using the plugin's settings panel. +\imageMacro{QmikPhotoacousticsImageProcessing_Settings.png,"The plugin's GUI",7.62} + +\subsection org_mitk_gui_qt_photoacoustics_imageprocessingBeamforming The Beamforming Settings +For beamforming, three beamforming algorithms are available: +
    +
  • DAS (Delay And Sum) +
  • DMAS (Delay Multiply And Sum) +
  • sDMAS (signed Delay Multiply And Sum) +
+Each of those can be coupled with either spherical delay calculation or a quadratic approximation for the delays. To supress noise, one of the following apodizations can be chosen to be used when beamforming: +
    +
  • Box (No apodization) +
  • Hamming +
  • Von Hann +
+Other Standard beamforming parameters are available, which have to be chosen depending on the source image to attain a correctly reconstructed image. +The Plugin is able to calculate the used scan depth as well as the transducer pitch from the selected image if the time-axis spacing is in microseconds, and the horizontal spacing in mm. If such a spacing is given, +check the box "Auto Get Depth" to make the plugin read those values by itself. +If the US source or the laser used for imaging is not located at the top of the image, an option is given to cut off pixels at the top of the image until the source. This value should be calibrated by the user +to match the used hardware. +If one wishes to beamform only certain slices of a given image, those can be selected by checking "select slices" and setting the "min" and "max" values accordingly, which are to be understood as closed interval boundaries. + +\subsection org_mitk_gui_qt_photoacoustics_imageprocessingBandpass The Bandpass Settings +The bandpass uses an itk implementation of an 1D Fast Fourier Transform (FFT) to transform the image vertically, then filters the image using a Tukey window in the frequency domain and performs an inverse 1D FFT to get the filtered image. +The "smoothness" of the tukey window can be chosen by using the "Tukey window alpha" parameter. The Tukey window interpolates between a Box window (alpha = 0) and a Von Hann window (alpha = 1). +The filtered frequencies can be set by defining the High and Low pass frequencies. + +\subsection org_mitk_gui_qt_photoacoustics_imageprocessingCrop The Crop Filter Settings +The crop filter cuts off parts of the image at the top and the bottom. The amount of pixels cut off can be configured using the "Cut Top" and "Cut Bottom" parameters. + +\subsection org_mitk_gui_qt_photoacoustics_imageprocessingBMode The BMode Filter Settings +The B-mode filters available are:
    -
  • Increases productivity -
  • Creates beautiful images -
  • Generates PhD thesis -
  • Brings world peace +
  • An absolute filter +
  • An envelope detection filter
+If desired, the filter can also resample the image to a given spacing; to do this, check the "Do Resampling" box and set the desired spacing in mm. +Afterwards a logarithmic filter can be applied, if "Add Logfilter" is checked. +\subsection org_mitk_gui_qt_photoacoustics_imageprocessingBatch Batch Processing +When processing large amounts of data, an option is available to automatically process multiple images by applying all filters in order to those images and saving the resulting images. +In the first row of the Batch Processing Panel one can select which filters should be applied to the image; in the second row one can select whether the resulting image from the filter should be saved. +After pressing the "Start Batch Processing" button, one can choose first the images to be processed, and then the folder where they will be saved. */ diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/QmikPhotoacousticsImageProcessing_DataManager.png b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/QmikPhotoacousticsImageProcessing_DataManager.png new file mode 100644 index 0000000000..29b7b0e002 Binary files /dev/null and b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/QmikPhotoacousticsImageProcessing_DataManager.png differ diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/QmikPhotoacousticsImageProcessing_Settings.png b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/QmikPhotoacousticsImageProcessing_Settings.png new file mode 100644 index 0000000000..f8210298cf Binary files /dev/null and b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/QmikPhotoacousticsImageProcessing_Settings.png differ diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/icon.xpm b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/icon.xpm deleted file mode 100644 index 9057c20bc6..0000000000 --- a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/icon.xpm +++ /dev/null @@ -1,21 +0,0 @@ -/* XPM */ -static const char * icon_xpm[] = { -"16 16 2 1", -" c #FF0000", -". c #000000", -" ", -" ", -" ", -" ", -" ", -" ", -" ", -" ", -" ", -" ", -" ", -" ", -" ", -" ", -" ", -" "}; diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/pai.png b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/pai.png new file mode 100644 index 0000000000..1b8dc34c11 Binary files /dev/null and b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/pai.png differ diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/resources/pai.png b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/resources/pai.png new file mode 100644 index 0000000000..1b8dc34c11 Binary files /dev/null and b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/resources/pai.png differ 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 8c59dee114..84c5f9668f 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 @@ -1,1080 +1,1161 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ // Blueberry #include #include // Qmitk #include "PAImageProcessing.h" // Qt #include #include #include #include //mitk image #include #include "mitkPhotoacousticImage.h" #include "mitkPhotoacousticBeamformingFilter.h" //other #include #include #include const std::string PAImageProcessing::VIEW_ID = "org.mitk.views.paimageprocessing"; -PAImageProcessing::PAImageProcessing() : m_ResampleSpacing(0), m_UseLogfilter(false) +PAImageProcessing::PAImageProcessing() : m_ResampleSpacing(0), m_UseLogfilter(false), m_FilterBank(mitk::PhotoacousticImage::New()) { qRegisterMetaType(); qRegisterMetaType(); } void PAImageProcessing::SetFocus() { m_Controls.buttonApplyBModeFilter->setFocus(); } void PAImageProcessing::CreateQtPartControl(QWidget *parent) { // 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(UpdateBounds())); - connect(m_Controls.boundHigh, SIGNAL(valueChanged(int)), this, SLOT(UpdateBounds())); - connect(m_Controls.Partial, SIGNAL(clicked()), this, SLOT(UpdateBounds())); + 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{'/'}; - mitk::PhotoacousticImage::Pointer filterbank = mitk::PhotoacousticImage::New(); - 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::LoadImage(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 = filterbank->ApplyBeamforming(image, BFconfig, m_Controls.Cutoff->value(), progressHandle); + 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 = filterbank->ApplyCropping(image, m_Controls.CutoffAbove->value(), m_Controls.CutoffBelow->value(), 0, 0, 0, image->GetDimension(2) - 1); + 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.BPLowPass) { QMessageBox Msgbox; Msgbox.setText("HighPass higher than LowPass, disabled both."); Msgbox.exec(); BPHighPass = 0; BPLowPass = 0; } - image = filterbank->BandpassFilter(image, recordTime, BPHighPass, BPLowPass, m_Controls.BPFalloff->value()); + image = m_FilterBank->BandpassFilter(image, recordTime, BPHighPass, BPLowPass, m_Controls.BPFalloff->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"); - - if (m_Controls.BModeMethod->currentText() == "Simple Abs Filter") - image = filterbank->ApplyBmodeFilter(image, mitk::PhotoacousticImage::BModeMethod::Abs, m_UseLogfilter, m_ResampleSpacing); - else if (m_Controls.BModeMethod->currentText() == "Shape Detection") - image = filterbank->ApplyBmodeFilter(image, mitk::PhotoacousticImage::BModeMethod::ShapeDetection, m_UseLogfilter, m_ResampleSpacing); + bool useGPU = m_Controls.UseGPUBmode->isChecked(); + + if (m_Controls.BModeMethod->currentText() == "Absolute Filter") + image = m_FilterBank->ApplyBmodeFilter(image, mitk::PhotoacousticImage::BModeMethod::Abs, useGPU, m_UseLogfilter, m_ResampleSpacing); + else if (m_Controls.BModeMethod->currentText() == "Envelope Detection") + image = m_FilterBank->ApplyBmodeFilter(image, mitk::PhotoacousticImage::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->setCutoff(m_Controls.Cutoff->value()); thread->setInputImage(image); + thread->setFilterBank(m_FilterBank); MITK_INFO << "Started new thread for Beamforming"; thread->start(); } } } void PAImageProcessing::HandleBeamformingResults(mitk::Image::Pointer image) { auto newNode = mitk::DataNode::New(); newNode->SetData(image); // name the new Data node std::stringstream newNodeName; newNodeName << m_OldNodeName << " "; - if (BFconfig.Algorithm == mitk::BeamformingFilter::beamformingSettings::BeamformingAlgorithm::DAS) + if (BFconfig.Algorithm == mitk::BeamformingSettings::BeamformingAlgorithm::DAS) newNodeName << "DAS bf, "; - else if (BFconfig.Algorithm == mitk::BeamformingFilter::beamformingSettings::BeamformingAlgorithm::DMAS) + else if (BFconfig.Algorithm == mitk::BeamformingSettings::BeamformingAlgorithm::DMAS) newNodeName << "DMAS bf, "; - if (BFconfig.DelayCalculationMethod == mitk::BeamformingFilter::beamformingSettings::DelayCalc::QuadApprox) + if (BFconfig.DelayCalculationMethod == mitk::BeamformingSettings::DelayCalc::QuadApprox) newNodeName << "q. delay"; - if (BFconfig.DelayCalculationMethod == mitk::BeamformingFilter::beamformingSettings::DelayCalc::Spherical) + if (BFconfig.DelayCalculationMethod == 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); - auto data = newNode->GetData(); - levelWindow.SetAuto(dynamic_cast(data), true, true); + 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( - dynamic_cast(data)->GetGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true); + 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); - if(m_Controls.BModeMethod->currentText() == "Simple Abs Filter") - thread->setConfig(m_UseLogfilter, m_ResampleSpacing, mitk::PhotoacousticImage::BModeMethod::Abs); - else if(m_Controls.BModeMethod->currentText() == "Shape Detection") - thread->setConfig(m_UseLogfilter, m_ResampleSpacing, mitk::PhotoacousticImage::BModeMethod::ShapeDetection); + bool useGPU = m_Controls.UseGPUBmode->isChecked(); + if(m_Controls.BModeMethod->currentText() == "Absolute Filter") + thread->setConfig(m_UseLogfilter, m_ResampleSpacing, mitk::PhotoacousticImage::BModeMethod::Abs, useGPU); + else if(m_Controls.BModeMethod->currentText() == "Envelope Detection") + thread->setConfig(m_UseLogfilter, m_ResampleSpacing, mitk::PhotoacousticImage::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()); + 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.BPLowPass) { QMessageBox Msgbox; Msgbox.setText("HighPass higher than LowPass, disabled both."); Msgbox.exec(); BPHighPass = 0; BPLowPass = 0; } thread->setConfig(BPHighPass, BPLowPass, m_Controls.BPFalloff->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::UpdateBounds() +void PAImageProcessing::SliceBoundsEnabled() { if (!m_Controls.Partial->isChecked()) { m_Controls.boundLow->setEnabled(false); m_Controls.boundHigh->setEnabled(false); - BFconfig.partial = false; return; } else { m_Controls.boundLow->setEnabled(true); m_Controls.boundHigh->setEnabled(true); - BFconfig.partial = true; } +} - if(m_Controls.boundLow->value()>m_Controls.boundHigh->value()) +void PAImageProcessing::UpperSliceBoundChanged() +{ + if(m_Controls.boundLow->value() > m_Controls.boundHigh->value()) { - MITK_INFO << "high bound < low bound -> setting both to beamform only first slice"; - m_Controls.boundLow->setValue(0); - m_Controls.boundHigh->setValue(0); - BFconfig.CropBounds[0] = 0; - BFconfig.CropBounds[1] = 0; + m_Controls.boundLow->setValue(m_Controls.boundHigh->value()); } - else +} + +void PAImageProcessing::LowerSliceBoundChanged() +{ + if (m_Controls.boundLow->value() > m_Controls.boundHigh->value()) { - BFconfig.CropBounds[0] = m_Controls.boundLow->value(); - BFconfig.CropBounds[1] = 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); } - UpdateRecordTime(image); - // bandpass configs - float speedOfSound = m_Controls.BPSpeedOfSound->value(); // [m/s] - float recordTime = image->GetDimension(1)*image->GetGeometry()->GetSpacing()[1] / 1000 / speedOfSound; + m_Controls.boundLow->setMaximum(image->GetDimension(2) - 1); + m_Controls.boundHigh->setMaximum(image->GetDimension(2) - 1); + + UpdateBFSettings(image); + + m_Controls.CutoffBeforeBF->setValue(0.000001 / BFconfig.TimeSpacing); // 1us standard offset for our transducer std::stringstream frequency; - float maxFrequency = 1 / (recordTime / image->GetDimension(1)) * image->GetDimension(1) / 2 / 2 / 1000; + float maxFrequency = (1 / BFconfig.TimeSpacing) * 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.Algorithm = mitk::BeamformingFilter::beamformingSettings::BeamformingAlgorithm::DAS; + BFconfig.Algorithm = mitk::BeamformingSettings::BeamformingAlgorithm::DAS; else if ("DMAS" == m_Controls.BFAlgorithm->currentText()) - BFconfig.Algorithm = mitk::BeamformingFilter::beamformingSettings::BeamformingAlgorithm::DMAS; + BFconfig.Algorithm = mitk::BeamformingSettings::BeamformingAlgorithm::DMAS; + else if ("sDMAS" == m_Controls.BFAlgorithm->currentText()) + BFconfig.Algorithm = mitk::BeamformingSettings::BeamformingAlgorithm::sDMAS; if ("Quad. Approx." == m_Controls.DelayCalculation->currentText()) { - BFconfig.DelayCalculationMethod = mitk::BeamformingFilter::beamformingSettings::DelayCalc::QuadApprox; + BFconfig.DelayCalculationMethod = mitk::BeamformingSettings::DelayCalc::QuadApprox; } else if ("Spherical Wave" == m_Controls.DelayCalculation->currentText()) { - BFconfig.DelayCalculationMethod = mitk::BeamformingFilter::beamformingSettings::DelayCalc::Spherical; + BFconfig.DelayCalculationMethod = mitk::BeamformingSettings::DelayCalc::Spherical; } if ("Von Hann" == m_Controls.Apodization->currentText()) { - BFconfig.Apod = mitk::BeamformingFilter::beamformingSettings::Apodization::Hann; + BFconfig.Apod = mitk::BeamformingSettings::Apodization::Hann; } else if ("Hamming" == m_Controls.Apodization->currentText()) { - BFconfig.Apod = mitk::BeamformingFilter::beamformingSettings::Apodization::Hamm; + BFconfig.Apod = mitk::BeamformingSettings::Apodization::Hamm; } else if ("Box" == m_Controls.Apodization->currentText()) { - BFconfig.Apod = mitk::BeamformingFilter::beamformingSettings::Apodization::Box; + BFconfig.Apod = mitk::BeamformingSettings::Apodization::Box; } BFconfig.Pitch = m_Controls.Pitch->value() / 1000; // [m] BFconfig.SpeedOfSound = m_Controls.SpeedOfSound->value(); // [m/s] BFconfig.SamplesPerLine = m_Controls.Samples->value(); BFconfig.ReconstructionLines = m_Controls.Lines->value(); BFconfig.TransducerElements = m_Controls.ElementCount->value(); + BFconfig.apodizationArraySize = m_Controls.Lines->value(); BFconfig.Angle = m_Controls.Angle->value(); // [deg] BFconfig.UseBP = m_Controls.UseBP->isChecked(); - BFconfig.UseGPU = m_Controls.UseGPU->isChecked(); + BFconfig.UseGPU = m_Controls.UseGPUBf->isChecked(); + BFconfig.upperCutoff = m_Controls.CutoffBeforeBF->value(); - UpdateRecordTime(image); - UpdateBounds(); -} - -void PAImageProcessing::UpdateRecordTime(mitk::Image::Pointer image) -{ if (m_Controls.UseImageSpacing->isChecked()) { BFconfig.RecordTime = image->GetDimension(1)*image->GetGeometry()->GetSpacing()[1] / 1000000; // [s] BFconfig.TimeSpacing = image->GetGeometry()->GetSpacing()[1] / 1000000; - MITK_INFO << "Calculated Scan Depth of " << BFconfig.RecordTime * BFconfig.SpeedOfSound * 100 << "cm"; + MITK_INFO << "Calculated Scan Depth of " << BFconfig.RecordTime * BFconfig.SpeedOfSound * 100 / 2 << "cm"; } else { BFconfig.RecordTime = 2 * m_Controls.ScanDepth->value() / 1000 / BFconfig.SpeedOfSound; // [s] BFconfig.TimeSpacing = BFconfig.RecordTime / image->GetDimension(1); } if ("US Image" == m_Controls.ImageType->currentText()) { - BFconfig.Photoacoustic = false; + BFconfig.isPhotoacousticImage = false; } else if ("PA Image" == m_Controls.ImageType->currentText()) { - BFconfig.Photoacoustic = true; + BFconfig.isPhotoacousticImage = true; } + + BFconfig.partial = m_Controls.Partial->isChecked(); + BFconfig.CropBounds[0] = m_Controls.boundLow->value(); + BFconfig.CropBounds[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.Cutoff->setEnabled(true); + m_Controls.CutoffBeforeBF->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); - m_Controls.UseGPU->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.BPFalloff->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.Cutoff->setEnabled(false); + m_Controls.CutoffBeforeBF->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); - m_Controls.UseGPU->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.BPFalloff->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::PhotoacousticImage::Pointer filterbank = mitk::PhotoacousticImage::New(); + 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); }; - resultImage = filterbank->ApplyBeamforming(m_InputImage, m_BFconfig, m_Cutoff, progressHandle); + 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 result(resultImage); + emit message(errorMessage); } -void BeamformingThread::setConfig(mitk::BeamformingFilter::beamformingSettings BFconfig) +void BeamformingThread::setConfig(mitk::BeamformingSettings BFconfig) { m_BFconfig = BFconfig; } void BeamformingThread::setInputImage(mitk::Image::Pointer image) { m_InputImage = image; } -void BeamformingThread::setCutoff(int cutoff) -{ - m_Cutoff = cutoff; -} - void BmodeThread::run() { mitk::Image::Pointer resultImage; - mitk::PhotoacousticImage::Pointer filterbank = mitk::PhotoacousticImage::New(); - resultImage = filterbank->ApplyBmodeFilter(m_InputImage, m_Method, m_UseLogfilter, m_ResampleSpacing); + 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::PhotoacousticImage::BModeMethod method) +void BmodeThread::setConfig(bool useLogfilter, double resampleSpacing, mitk::PhotoacousticImage::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; - mitk::PhotoacousticImage::Pointer filterbank = mitk::PhotoacousticImage::New(); - resultImage = filterbank->ApplyCropping(m_InputImage, m_CutAbove, m_CutBelow, 0, 0, 0, m_InputImage->GetDimension(2) - 1); + 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) +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; - mitk::PhotoacousticImage::Pointer filterbank = mitk::PhotoacousticImage::New(); - resultImage = filterbank->BandpassFilter(m_InputImage, m_RecordTime, m_BPHighPass, m_BPLowPass, m_TukeyAlpha); + resultImage = m_FilterBank->BandpassFilter(m_InputImage, m_RecordTime, m_BPHighPass, m_BPLowPass, m_TukeyAlpha); emit result(resultImage); } void BandpassThread::setConfig(float BPHighPass, float BPLowPass, float TukeyAlpha, float recordTime) { m_BPHighPass = BPHighPass; m_BPLowPass = BPLowPass; m_TukeyAlpha = TukeyAlpha; 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 42270dd4c7..d20b78b3ae 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 @@ -1,182 +1,254 @@ /*=================================================================== 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" 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: - /// \brief Called when the user clicks the GUI button - - void UpdateBounds(); + void UpperSliceBoundChanged(); + void LowerSliceBoundChanged(); + void SliceBoundsEnabled(); void UseResampling(); void UseLogfilter(); void SetResampling(); void UseImageSpacing(); void UpdateImageInfo(); - void UpdateRecordTime(mitk::Image::Pointer image); + /** \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 + /** \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; - mitk::BeamformingFilter::beamformingSettings BFconfig; + /** \brief The settings set which is used for beamforming, updated through this class. + */ + mitk::BeamformingSettings 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::PhotoacousticImage::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::BeamformingFilter::beamformingSettings BFconfig); + void setConfig(mitk::BeamformingSettings BFconfig); void setInputImage(mitk::Image::Pointer image); - void setCutoff(int cutoff); + void setFilterBank(mitk::PhotoacousticImage::Pointer filterBank) + { + m_FilterBank = filterBank; + } + protected: - mitk::BeamformingFilter::beamformingSettings m_BFconfig; + mitk::BeamformingSettings m_BFconfig; mitk::Image::Pointer m_InputImage; int m_Cutoff; + + mitk::PhotoacousticImage::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::PhotoacousticImage::BModeMethod method); + void setConfig(bool useLogfilter, double resampleSpacing, mitk::PhotoacousticImage::BModeMethod method, bool useGPU); void setInputImage(mitk::Image::Pointer image); + void setFilterBank(mitk::PhotoacousticImage::Pointer filterBank) + { + m_FilterBank = filterBank; + } + protected: mitk::Image::Pointer m_InputImage; mitk::PhotoacousticImage::BModeMethod m_Method; bool m_UseLogfilter; double m_ResampleSpacing; + bool m_UseGPU; + + mitk::PhotoacousticImage::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); + void setConfig(unsigned int CutAbove, unsigned int CutBelow, unsigned int CutSliceFirst, unsigned int CutSliceLast); void setInputImage(mitk::Image::Pointer image); + void setFilterBank(mitk::PhotoacousticImage::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::PhotoacousticImage::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 TukeyAlpha, float recordTime); void setInputImage(mitk::Image::Pointer image); + void setFilterBank(mitk::PhotoacousticImage::Pointer filterBank) + { + m_FilterBank = filterBank; + } protected: mitk::Image::Pointer m_InputImage; float m_BPHighPass; float m_BPLowPass; float m_TukeyAlpha; float m_RecordTime; + + mitk::PhotoacousticImage::Pointer m_FilterBank; }; #endif // PAImageProcessing_h diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/PAImageProcessingControls.ui b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/PAImageProcessingControls.ui index bbc2c814b3..fcd6e415c8 100644 --- a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/PAImageProcessingControls.ui +++ b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/PAImageProcessingControls.ui @@ -1,960 +1,991 @@ PAImageProcessingControls 0 0 382 - 1217 + 1278 0 0 QmitkTemplate <html><head/><body><p><span style=" font-weight:600;">Batch Processing</span></p></body></html> Start Batch Processing Bandpass true Crop true Save true Save true Save Beamform true BMode true Save true <html><head/><body><p><span style=" font-weight:600;">B-mode Filter Settings</span></p></body></html> + + + + Absolute Filter + + + + Absolute Filter + + + + + Envelope Detection + + + + Do Resampling - - - - - - - Absolute Filter - - - - - Envelope Detection - - + + true + 0 0 13 0 11 + + 3 + 0.010000000000000 1.000000000000000 0.010000000000000 - 0.100000000000000 + 0.075000000000000 - [mm] Depth Spacing + [mm] Resampled Depth Spacing Add Logfilter + + + + Use GPU + + + QLabel { color: rgb(255, 0, 0) } <html><head/><body><p align="center"><span style=" font-size:10pt; font-weight:600;">Please select an image!</span></p></body></html> 0 0 Do image processing Apply B-mode Filter Qt::Horizontal <html><head/><body><p><span style=" font-weight:600;">Bandpass Filter Settings</span></p></body></html> QLayout::SetDefaultConstraint 0 0 0 3 0.010000000000000 200.000000000000000 15.000000000000000 [MHz] f High Pass [MHz] f Low Pass 0 0 3 200.000000000000000 - Thukey window alpha + Tukey window alpha 1 200.000000000000000 3000.000000000000000 5.000000000000000 - 1480.000000000000000 + 1540.000000000000000 [m/s] Speed of Sound 2 1.000000000000000 0.100000000000000 0.500000000000000 <html><head/><body><p align="center"><span style=" font-size:10pt; font-weight:600; color:#ff0000;">Please select an image!</span></p></body></html> Apply Bandpass Qt::Horizontal <html><head/><body><p><span style=" font-weight:600;">Crop Filter Settings</span></p></body></html> - - - + + + 99999 - - 5 - - 165 + 10 - - + + Cut Top - - + + + + Cut Bottom + + + + + 99999 - - 10 + + 5 - - - - - - Cut Bottom + + 165 <html><head/><body><p align="center"><span style=" font-size:10pt; font-weight:600; color:#ff0000;">Please select an image!</span></p></body></html> Apply Crop Filer Qt::Horizontal <html><head/><body><p><span style=" font-weight:600;">Beamforming Filter Settings</span></p></body></html> 5 2 Delay Calculation Auto Get Depth true Apply Beamforming Beamforming Method [mm] Scan Depth 0 0 - 2 + 3 0.010000000000000 9.000000000000000 0.050000000000000 0.300000000000000 Transducer Elements 0 0 4 300.000000000000000 0.100000000000000 50.000000000000000 [mm] Transducer Pitch 0 0 64 1024 128 128 0 0 256 16384 256 2048 0 0 64 2048 128 256 Samples Reconstruction Lines true 0 0 100 0 - + 0 0 900 10 0 - - - - Cutoff Upper Voxels - - - 0 0 DAS DMAS + + + sDMAS + + 0 0 + + Quad. Approx. + Quad. Approx. Spherical Wave 0 0 PA Image US Image Image Type 0 0 Von Hann Hamming Box Apodization 0 0 1 200.000000000000000 3000.000000000000000 5.000000000000000 - 1480.000000000000000 + 1540.000000000000000 [m/s] Speed of Sound false 99999 minimal beamformed slice min false 99999 10 Maximal beamformed slice max select slices - + Compute On GPU true true Auto Use Bandpass 0 0 1 1.000000000000000 180.000000000000000 27.000000000000000 [°] Element Angle + + + + Cutoff Upper Voxels + + + + + + + <html><head/><body><p align="center"><span style=" font-size:10pt; font-weight:600; color:#ff0000;">Please select an image!</span></p></body></html> + + + diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.photoacoustics.simulation/documentation/UserManual/Manual.dox deleted file mode 100644 index e9e31e8451..0000000000 --- a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/documentation/UserManual/Manual.dox +++ /dev/null @@ -1,12 +0,0 @@ -/** -\page org_mitk_gui_qt_photoacousticsimulation Photoacoustic Tissue Generator - -\imageMacro{icon.png,"Icon of Photoacousticsimulation", 2.00} - -\tableofcontents - -\section org_mitk_gui_qt_photoacousticsimulationOverview Overview - -TODO Describe this!! - -*/ diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/documentation/UserManual/icon.xpm b/Plugins/org.mitk.gui.qt.photoacoustics.simulation/documentation/UserManual/icon.xpm deleted file mode 100644 index d6f2f2a34b..0000000000 --- a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/documentation/UserManual/icon.xpm +++ /dev/null @@ -1,203 +0,0 @@ -/* XPM */ -static char * icon_xpm[] = { -"128 128 72 1", -" c None", -". c #484848", -"+ c #2E2E2E", -"@ c #272727", -"# c #242424", -"$ c #202020", -"% c #171717", -"& c #1C1C1C", -"* c #1A1A1A", -"= c #191919", -"- c #222222", -"; c #292929", -"> c #404040", -", c #313131", -"' c #1B1B1B", -") c #0E0E0E", -"! c #070707", -"~ c #000000", -"{ c #0A0A0A", -"] c #111111", -"^ c #282828", -"/ c #2D2D2D", -"( c #050505", -"_ c #010101", -": c #0D0D0D", -"< c #151515", -"[ c #1E1E1E", -"} c #080808", -"| c #030303", -"1 c #020202", -"2 c #1D1D1D", -"3 c #0C0C0C", -"4 c #2F2F2F", -"5 c #181818", -"6 c #161616", -"7 c #232323", -"8 c #262626", -"9 c #212121", -"0 c #121212", -"a c #040404", -"b c #323232", -"c c #252525", -"d c #0B0B0B", -"e c #3C3C3C", -"f c #131313", -"g c #090909", -"h c #1F1F1F", -"i c #060606", -"j c #2C2C2C", -"k c #141414", -"l c #3A3A3A", -"m c #2A2A2A", -"n c #333333", -"o c #3B3B3B", -"p c #3D3D3D", -"q c #101010", -"r c #373737", -"s c #0F0F0F", -"t c #3E3E3E", -"u c #343434", -"v c #353535", -"w c #414141", -"x c #383838", -"y c #303030", -"z c #393939", -"A c #424242", -"B c #2B2B2B", -"C c #454545", -"D c #3F3F3F", -"E c #4D4D4D", -"F c #4B4B4B", -"G c #363636", -" ", -" .+@#$%&*=-;> ", -" ,')!~~~~~~~~~~~~~{]^ ", -" /*](~~~~~~~~~__~~~~_~~~~_:<[ ", -" ^}|~_~~~~___~~~__~~~_~~_~~~~~11* ", -" ^!~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~2 ", -" '3~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~(% ", -" 4!_~~~_~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~_~~~15 ", -" -~~~~_~~~~~~~~_(!}65&[7892&0}}a_~~~~~~~~~~~~~{b ", -" +)~~~~~~_~~~~~3'$ c$d~~~~~~~~~~~~~6 ", -" c~~~~~~~~~~~1[e ef_~~~~~~~~~~~g ", -" h~~_~~~~~~~}2 f!_~~~~~~~~~1 ", -" %_~~~~~~~~38 -i~~_~~~~~~(j ", -" k~~~~~~~~~7 [~~_~~~~~~_b ", -" =~~~~~~~_3l @g~~~~~~~~~m ", -" ;1~_~~~~~9 &_~~~~~~~( ", -" e_~~~~~~1n b1~~~~~~~a ", -" i~~~~~~{o p{~_~~~~~} ", -" f~~~~~~: q~~~~~_~k ", -" ,~~~~~~: q~~~~~_~/ ", -" !~~~~~g 0~~~~~~i ", -" <~~~~~|o :~~~~~~6 ", -" |~~~~~r (~~~~~1 ", -" 6~~~~~& g~~~~~] ", -" (~~~~! 4a_~~_1r ", -" 2~~~~~j h~~~~~s ", -" ~~~~~2 k~~~~~t ", -" *~~~~{ g~~~~s ", -" a~~~~7 8_~_~| ", -" a~~~! 3~~__2 ", -" *~~~~2 u~~~~!q@ ", -" q~~~~~1 _~_~~_( ", -" i~_~~~~, [~~~~~_| ", -" a~~~~~~& &~~~~_~18 ", -" c_~~~~~~v >~~~~~_~5 ", -" h_~~~~~~ |_~~_~~f ", -" k_~__~~) 5~~_~~_( ", -" d~~_~~~h ^~_~~~~1 ", -" 51_~~~~, w~~~~~|7 ", -" %~~{q) ^9/{~! ", -" d~| =~( ", -" i~} _11_1_ '~a ", -" !~d ~~~~~~~~~~~~~~~~~ ;_| ", -" !~] ~~~~~~~~~~~~~~~~~~~~~ /11 ", -" i~< i~~~~~~~ ~~~~~~~~ x11# ", -" i~5 ~~~~~~ ~~~~~~ w11 ", -" |_* ~~~~~~~ ~~~~~~ t11 ", -" a~' ~~~~~~ ~~~~ y11+ ", -" 9-y1~* z@ ~~~~~ ~~~a 8:<-u j1~3}i7 ", -" $~~~~~5 61~~_# ~~~~~ ~~~~ 6~~~~~% h_~~_~d ", -" 6~_~_~5 f~~~_~~w ~~~~ ~~~~ ~~~~~~_n '~~~~~} ", -" =~~_~_5 i~~~~~~4 ~~~~ ~~~~ A~~~~~~~[ %~___~) ", -" *~~~~~5 b@'~__~~~~7 ~~~~ ~~~~ ;~~~~~~~~~i9A<~~_~~s ", -" =~~~~~{'}~~~~~~~~~~[ ~~~~ ~~~ 8~~~~~~~~~~~~~_~_~~f ", -" &~~~~~~~_~~~~~~~~~~k ~~~ ~~~ [~~~~_~~~~~_~~~~~~~& ", -" c~~~~~~~~~~~~~~~~~~| ~~~~ ~~~ k~~~~~~~~~~~~~~~~~~2 ", -" B_~~~~~~~~~~~~~~~~~~ ~~~ ~~~ 3~~~~~~~~~~~~~~~~~~* ", -" B|~~~~~~~~~~~~~~~~~~ ~~~ ~~~ |~~~~~~~~~~~~~~~~~~[ ", -" a~~~~~~~~~~~~~~~~~~e~~~ ~~~ ~~~~~~~~~~~~~~~~~~~[ ", -" [_~~~~~~~~~~~~~~~~~~$|~~ ~~m~~~~~~~~~~~~~~~~~~~} ", -" |~~~~~~~~~~~~~~~~~~~ka~ ~~-~~~~~~~~~~~~~~~~_~_~* ", -" h~_~~~~~~~~~~~~~~~~~~f}~ ~|9~~~~~~~~~~~~~~~~~~~~~ ", -" |~~~~~~~~~~~~~~~~~~~~0)~ ~(*~~~~~~~~~~~~~~~~~~~~~= ", -" ^~~~~~~~~~~~~~~~~~~~~~qs_ ~if~~~~~~~~~~~~~~~~~~~~~} ", -" <~~~~~~~~~~~~~~~~~~~~_d3_ ~!q~~~~~~~~~~~~~~~~~~~~~! ", -" ]~~~~~~~~~~~~~~~~~~~~~{{_ ~~ ~~_~~~_~~~ ~{]~~~~~~~~~~~~~~~~~~~~~( ", -" h~~~~~~~~~~~~~~~~~~~__{s1 ~~~~~~~~~~~~~~~~~~~~~~~ ~:]~~~~~~~~~~~~~~~~~~~~~i ", -" &~~~~~~~~~~~~~~~~~~~~_i=~ ~~~~~~~~~~~1 _~~ _~~~~ _)0~~~~~~~~~~~~~~~~~~~~~i ", -" 2~~~~~~~~~~~~~~~~~~~~_|*~ ~~~ ~~ ~~ ~~~ _d:_~~~~~~~~~~~~~~~~~~~~} ", -" 9~~~~~~~~~~~~~~~~~~~~~~%_ ~~ ~~ ~~ ~~ _{d_~~~~~~~~~~~~~~~~~~~~{ ", -" n~~~~~~~~~~~~~~~~~~~~~~'~ ~~~ ~~ ~~~ ~~~ _fg~~~~~~~~~~~~~~~~~~~~~s ", -" C~~~~~~~~~~~~~~~~~~~~~~#~ ~~ ~~ ~~ ~~ ~[i_~~~~~~~~~~~~~~~~~~~~k ", -" D~~~~~~~~~~~~~~~~~~~~~~'(_ ~~ ~~ ~~ ~~ ~2~~~~~~~~~~~~~~~~~~~~~~k ", -" ~~~~~~~~~~~~~~~~~~~~~~fg~ ~~~ ~~~ ~~ ~~~ ~~*~~~~~~~~~~~~~~~~~~~~~~5 ", -" ~~~~~~~~~~~~~~~~~~~~_~)q~ ~~ ~~ ~~_ ~~ _~9~~~~~~~~~~~~~~~~~~~~~~B ", -" _~~~~~~~~~~~~~~~~~~~~_g&~~ ~~~ ~~~~~~~~ ~~~ _~7~__~~~~~~~~~~~~~~~~~~~l ", -" g~~~~~~~~~~~~~~~~~~~~_~8~~ ~~~ ~~~~~~~~ ~~ ~~i7~~~~~~~~~~~~~~~~~~~~~~> ", -" %~~~~~~~~~~~~~~~~~~~__~9~~~ ~~ ~~~~~~~ ~~~ ~~~ ]~~~~~~~~~~~~~~~~~~~~~~ ", -" '~~~~~~~~~~~~~~~~~~~~~~#~~~ ~~~ ~~ ~1 ~~~ ~~~ g~~~~~~~~~~~~~~~~~~~~~1 ", -" #~~~~~~~~~~~~~~~~~~~__~B|~~~ ~~~ ~~~~1 ~~~ ~~~ i~~~~~~~~~~~~~~~~~~~~~{ ", -" v~~~~~~~~~~~~~~~~~~~__~9 ~~~ ~~ ~~~~1 ~~~ ~~~ _~~~~~~~~~~~~~~~~~~~~~0 ", -" E~~~~~~~~~~~~~~~~~~~~~~{ ~~~ ~~~ ~~~~ ~~ ~~~~ F~~~~~~~~~~~~~~~~~~~~~~$ ", -" i_~~~~~~~~~~~~~~~~~~~~( ~~~ ~~ ~~~~ ~~~ ~~~ v~~~~~~~~~~~~~~~~~~~~~~G ", -" %~~~~~~~~~~~~~~~~~~~~~| ~~~~ ~~_~~~~1~~ ~~~ 8~_~~~~~~~~~~~~~~~~~~~{ ", -" 7~~~~~~~~~~~~~~~~~~~~~~ ~~~ _~~~~~~_~~ ~~~ 7~~~~~~~~~~~~~~~~~~_~_h ", -" g~~~~~~~~~~~~~~~~~~~~~4 ~~~~ ~~~~~~~~~~ ~~~ 2~_~~~~~~~~~~~~~~~~~~i ", -" y~_~~~~~~~~~~~~~~~~~~~9 ~~~ ~~~~~~~~~~_ ~~~ 0~~~~~~~~~~~~~~~~~~_~@ ", -" c~~~~~~~~~~~~~~~~~~~~9 ~~~~ ~~~ ~~_ ~~~ }~~~~~~~~~~~~~~~~~~~2 ", -" :~~~~~~~~~~~~~~~~~~~[ ~~~ ~~ __~ ~~_ ~~~ _~~~~~~~~~~~~~~~~~~~9 ", -" <~~_~~~~~~~~~~~~~~~~f ~~~~ ~~ ~i ~ ~~_ ~~~ _~~~~~~~~~_~~~~_~_~~~ ", -" 6~~__~__~~~~~~~~~~~~s ~~~ ~~~~~|~~~~ ~~~ 1~~~~~~~~~~_~~~1ki_3 ", -" 0sh2:~~~~~~~~~~~~~~: ~~~ ~~~~~~~~~~ ~~~ b_~~~~~~~~~~~~{5 7 ", -" v2!~~~~~~~~~~~3 ~~~ ~~__~~~~~~ ~~~ ~~~~~~~dsds#u ", -" >y+l'~~~~~_$ ~~~ ~~1 ~~~_~~ ~~ #___~~s ", -" 6diq09 ~~~ ~~1 ~ ~ ~~ ~~~ #$=[ ", -" _~~ ~~1 ~ ~ ~~ _~~ ", -" ~~ ~~_ ~ ~1~~ ~~_ ", -" ~~ ~~~ ~ ~ ~~ ~~_ ", -" ~~ ~~~ ~ ~ ~~ ~~_ ", -" ~~_ ~~~ ~ ~ ~~ ~~~ ", -" ~~~ _~~~ ~ ~ ~~ ~~~ ", -" ~~~~ 1~~ ~ ~ ~~ ~~~~ ", -" ~~~~~~~~~~_~~~~~~~_~~~~~~~ ", -" ~~~~~~~~~~~~~~~~~~~~~~~~~~ ", -" ~~~~~~~~~~~~~~~~~~~~~~_1 ", -" 6~~~~~~~~~~~~~~~~~~~~q ", -" ]~~~~~~~~~~~~~~~~~~~~q ", -" ~~~~~~~~~~~~~~~~~~~~~d ", -" B~~~~~~~~~~~~~~~~~~~~d ", -" #~~~~~~~~~~~~~~~~~~~_6 ", -" _~~~~~~~~~~~~~~~~~~~| ", -" _~~~~~~~~~~~~~~~~~~_6 ", -" ^_~~~~~~~~~~~~~~~~~~_% ", -" |~~~~~~~~~~~~_1~1~~~1 ", -" 1~~~~~~~~~~~~~~~~~~_& ", -" @_~~~~~~~~~~~~~~~~~~_% ", -" |~~~~~~~~~~~~~~~~~~~_ ", -" dggggggggggggggggggg% ", -" #_~~~~~~~~~~~~~~~~~~~' ", -" =~~~~~~~~~~~~~~__~~~1 ", -" f~~~~~~~~~~~~:a(1~~{ ", -" *~~~~~~~~~~~~~~~~] ", -" 71~~~~~~~~~~~~~q ", -" [_~~~~~~~~~~_9 ", -" 7~~~~~~~~~1h ", -" @~~~~~~~~0 ", -" j##h1]7B ", -" "}; diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/documentation/doxygen/modules.dox b/Plugins/org.mitk.gui.qt.photoacoustics.simulation/documentation/doxygen/modules.dox deleted file mode 100644 index 1032079a00..0000000000 --- a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/documentation/doxygen/modules.dox +++ /dev/null @@ -1,16 +0,0 @@ -/** - \defgroup org_mitk_gui_qt_photoacousticsimulation org.mitk.gui.qt.photoacousticsimulation - \ingroup MITKPlugins - - \brief Describe your plugin here. - -*/ - -/** - \defgroup org_mitk_gui_qt_photoacousticsimulation_internal Internal - \ingroup org_mitk_gui_qt_photoacousticsimulation - - \brief This subcategory includes the internal classes of the org.mitk.gui.qt.photoacousticsimulation plugin. Other - plugins must not rely on these classes. They contain implementation details and their interface - may change at any time. We mean it. -*/