diff --git a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASImageSource.cpp b/Modules/US/USHardwareDiPhAS/mitkUSDiPhASImageSource.cpp index 3866134eb4..8975ee7a81 100644 --- a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASImageSource.cpp +++ b/Modules/US/USHardwareDiPhAS/mitkUSDiPhASImageSource.cpp @@ -1,931 +1,899 @@ /*=================================================================== 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. ===================================================================*/ // std dependencies #include #include #include // mitk dependencies #include "mitkUSDiPhASDevice.h" #include "mitkUSDiPhASImageSource.h" #include #include "mitkUSDiPhASBModeImageFilter.h" #include "ITKUltrasound/itkBModeImageFilter.h" #include "mitkImageCast.h" #include "mitkITKImageImport.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" mitk::USDiPhASImageSource::USDiPhASImageSource(mitk::USDiPhASDevice* device) : m_Device(device), m_StartTime(((float)std::clock()) / CLOCKS_PER_SEC), m_UseGUIOutPut(false), m_DataType(DataType::Image_uChar), m_GUIOutput(nullptr), m_UseBModeFilter(false), m_CurrentlyRecording(false), m_DataTypeModified(true), m_DataTypeNext(DataType::Image_uChar), m_CurrentImageTimestamp(0), m_PyroConnected(false), - m_ImageTimestampBuffer(), m_VerticalSpacing(0), m_UseBModeFilterModified(false), m_UseBModeFilterNext(false), m_ScatteringCoefficientModified(false), m_CompensateForScatteringModified(false), m_VerticalSpacingModified(false), m_ScatteringCoefficient(15), m_CompensateForScattering(false), m_CompensateEnergy(false), m_CompensateEnergyNext(false), m_CompensateEnergyModified(false) { m_BufferSize = 100; m_ImageTimestampBuffer.insert(m_ImageTimestampBuffer.begin(), m_BufferSize, 0); m_LastWrittenImage = m_BufferSize - 1; - m_ImageBuffer.insert(m_ImageBuffer.begin(), m_BufferSize, nullptr); + m_ImageBuffer.insert(m_ImageBuffer.begin(), m_BufferSize, std::pair(nullptr, nullptr)); us::ModuleResource resourceFile; std::string name; m_FluenceCompOriginal.insert(m_FluenceCompOriginal.begin(), 5, Image::New()); for (int i = 5; i <= 25; ++i) { name = "c:\\HomogeneousScatteringAssumptions\\Scattering" + std::to_string(i) + ".nrrd"; m_FluenceCompOriginal.push_back(mitk::IOUtil::LoadImage(name)); } m_FluenceCompResized.insert(m_FluenceCompResized.begin(), 26, Image::New()); m_FluenceCompResizedItk.insert(m_FluenceCompResizedItk.begin(), 26, itk::Image::New()); } mitk::USDiPhASImageSource::~USDiPhASImageSource() { // close the pyro MITK_INFO("Pyro Debug") << "StopDataAcquisition: " << m_Pyro->StopDataAcquisition(); MITK_INFO("Pyro Debug") << "CloseConnection: " << m_Pyro->CloseConnection(); m_PyroConnected = false; m_Pyro = nullptr; } -void mitk::USDiPhASImageSource::GetNextRawImage(std::vector& imageVector) +void mitk::USDiPhASImageSource::CheckModifiedVariables() { // modify all settings that have been changed here, so we don't get multithreading issues if (m_DataTypeModified) { SetDataType(m_DataTypeNext); m_DataTypeModified = false; UpdateImageGeometry(); } if (m_UseBModeFilterModified) { SetUseBModeFilter(m_UseBModeFilterNext); m_UseBModeFilterModified = false; } if (m_VerticalSpacingModified) - { + { m_VerticalSpacing = m_VerticalSpacingNext; m_VerticalSpacingModified = false; } if (m_ScatteringCoefficientModified) { m_ScatteringCoefficient = m_ScatteringCoefficientNext; m_ScatteringCoefficientModified = false; } if (m_CompensateForScatteringModified) { m_CompensateForScattering = m_CompensateForScatteringNext; m_CompensateForScatteringModified = false; } if (m_CompensateEnergyModified) { m_CompensateEnergy = m_CompensateEnergyNext; m_CompensateEnergyModified = false; } +} + +void mitk::USDiPhASImageSource::ResizeFluenceImage(mitk::Vector3D spacing, unsigned int* dimensions) +{ + auto curResizeImage = ApplyResampling(m_FluenceCompOriginal.at(m_ScatteringCoefficient), spacing, dimensions); + + unsigned int imageSize = dimensions[0] * dimensions[1]; + double* rawOutputData = new double[imageSize]; + double* rawScatteringData = (double*)curResizeImage->GetData(); + + //everything above 1.5mm is still inside the transducer; therefore the fluence compensation image has to be positioned a little lower + float upperCutoffmm = 1.5; + unsigned int lowerBound = std::round(upperCutoffmm / spacing[1])*dimensions[0]; + unsigned int upperBound = lowerBound + imageSize; + for (unsigned int i = 0; i < lowerBound && i < imageSize; ++i) + { + rawOutputData[i] = 0; // everything than cannot be compensated shall be treated as garbage, here the upper 0.15mm + } + for (unsigned int i = lowerBound; i < upperBound && i < imageSize; ++i) + { + rawOutputData[i] = 1 / rawScatteringData[i - lowerBound]; + } + for (unsigned int i = upperBound; i < imageSize; ++i) + { + rawOutputData[i] = 0; // everything than cannot be compensated shall be treated as garbage + } + + unsigned int dim[] = { dimensions[0], dimensions[1], 1 }; + curResizeImage->Initialize(mitk::MakeScalarPixelType(), 3, dim); + curResizeImage->SetSpacing(spacing); + curResizeImage->SetImportSlice(rawOutputData, 0, 0, 0, mitk::Image::ManageMemory); + + mitk::CastToItkImage(curResizeImage, m_FluenceCompResizedItk.at(m_ScatteringCoefficient)); + m_FluenceCompResized.at(m_ScatteringCoefficient) = mitk::GrabItkImageMemory(m_FluenceCompResizedItk.at(m_ScatteringCoefficient)); + + MITK_INFO << "Resized a fluence image."; +} + +void mitk::USDiPhASImageSource::GetNextRawImage(std::vector& imageVector) +{ + CheckModifiedVariables(); if (imageVector.size() != 2) { imageVector.resize(2); } // make sure image is nullptr - mitk::Image::Pointer image = nullptr; + mitk::Image::Pointer imageUS = nullptr; + mitk::Image::Pointer imagePA = nullptr; float ImageEnergyValue = 0; - for (int i = 100; i > 90 && ImageEnergyValue <= 0; --i) + for (int i = 100; i > 0 && ImageEnergyValue <= 0; --i) { if (m_ImageTimestampBuffer[(m_LastWrittenImage + i) % 100] != 0) { ImageEnergyValue = m_Pyro->GetClosestEnergyInmJ(m_ImageTimestampBuffer[(m_LastWrittenImage + i) % 100]); if (ImageEnergyValue > 0) { - image = &(*m_ImageBuffer[(m_LastWrittenImage + i) % 100]); + imagePA = m_ImageBuffer[(m_LastWrittenImage + i) % 100].first; + imageUS = m_ImageBuffer[(m_LastWrittenImage + i) % 100].second; } } } // if we did not get any usable Energy value, compensate using this default value - if (image == nullptr) + if (imagePA == nullptr || imageUS == nullptr) { - image = &(*m_ImageBuffer[m_LastWrittenImage]); - ImageEnergyValue = 40; - if (image == nullptr) + imagePA = m_ImageBuffer[m_LastWrittenImage].first; + imageUS = m_ImageBuffer[m_LastWrittenImage].second; + ImageEnergyValue = 1; + if (imagePA == nullptr || imageUS == nullptr) return; } // do image processing before displaying it - if (image.IsNotNull()) + if(imagePA.IsNotNull() && m_DataType == DataType::Beamformed_Short) { itkFloatImageType::Pointer itkImage; - mitk::CastToItkImage(image, itkImage); - image = mitk::GrabItkImageMemory(itkImage); //thereby using float images - image = CutOffTop(image, 165); - - // now apply filters to the image, if the options have been selected. - if ((m_CompensateForScattering || m_UseBModeFilter) && m_DataType == DataType::Beamformed_Short) - { - if (m_Device->GetScanMode().beamformingAlgorithm == Beamforming::PlaneWaveCompound) // this is for ultrasound only mode - { - if (m_UseBModeFilter) - { - image = ApplyBmodeFilter(image, true); - if (m_VerticalSpacing) - image = ResampleOutputVertical(image, m_VerticalSpacing); - } - } - - else - { - Image::Pointer imagePA = Image::New(); - unsigned int dim[] = { image->GetDimension(0),image->GetDimension(1),1}; - imagePA->Initialize(image->GetPixelType(), 3, dim); - imagePA->SetGeometry(image->GetGeometry()); + mitk::CastToItkImage(imagePA, itkImage); + imagePA = mitk::GrabItkImageMemory(itkImage); //thereby using float images + imagePA = CutOffTop(imagePA, 165); - Image::Pointer imageUS = Image::New(); - imageUS->Initialize(image->GetPixelType(), 3, dim); - imageUS->SetGeometry(image->GetGeometry()); + if (m_CompensateEnergy) + imagePA = MultiplyImage(imagePA, 1 / ImageEnergyValue); // TODO: add the correct prefactor here - ImageReadAccessor inputReadAccessorCopyPA(image, image->GetSliceData(0)); - imagePA->SetSlice(inputReadAccessorCopyPA.GetData(), 0); - ImageReadAccessor inputReadAccessorCopyUS(image, image->GetSliceData(1)); - imageUS->SetSlice(inputReadAccessorCopyUS.GetData(), 0); + if (m_UseBModeFilter) + imagePA = ApplyBmodeFilter(imagePA, false); - // first, seperate the PA image from the USImages - - // then, we compensate the PAImage using our ImageEnergyValue - if(m_CompensateEnergy) - imagePA = MultiplyImage(imagePA, 1/ImageEnergyValue); // TODO: add the correct prefactor here!!!! - - // now we apply the BModeFilter - if (m_UseBModeFilter) - { - imageUS = ApplyBmodeFilter(imageUS, true); // the US Images get a logarithmic filter - imagePA = ApplyBmodeFilter(imagePA, false); - } - - ImageReadAccessor inputReadAccessorPA(imagePA, imagePA->GetSliceData(0)); - image->SetSlice(inputReadAccessorPA.GetData(), 0); - ImageReadAccessor inputReadAccessorUS(imageUS, imageUS->GetSliceData(0)); - image->SetSlice(inputReadAccessorUS.GetData(), 1); - if (m_VerticalSpacing) - { - image = ResampleOutputVertical(image, m_VerticalSpacing); - } - - // and finally the scattering corrections - if (m_CompensateForScattering) - { - auto curResizeImage = m_FluenceCompResized.at(m_ScatteringCoefficient); // just for convenience + if (m_VerticalSpacing) + imagePA = ResampleOutputVertical(imagePA, m_VerticalSpacing); - // update the fluence reference images! - bool doResampling = image->GetDimension(0) != curResizeImage->GetDimension(0) || image->GetDimension(1) != curResizeImage->GetDimension(1) - || image->GetGeometry()->GetSpacing()[0] != curResizeImage->GetGeometry()->GetSpacing()[0] || image->GetGeometry()->GetSpacing()[1] != curResizeImage->GetGeometry()->GetSpacing()[1]; - if (doResampling) - { - curResizeImage = ApplyResampling(m_FluenceCompOriginal.at(m_ScatteringCoefficient), image->GetGeometry()->GetSpacing(), image->GetDimensions()); - - double* rawOutputData = new double[image->GetDimension(0)*image->GetDimension(1)]; - double* rawScatteringData = (double*)curResizeImage->GetData(); - int sizeRawScatteringData = curResizeImage->GetDimension(0) * curResizeImage->GetDimension(1); - int imageSize = image->GetDimension(0)*image->GetDimension(1); - - //everything above 1.5mm is still inside the transducer; therefore the fluence compensation image has to be positioned a little lower - float upperCutoffmm = 1.5; - int lowerBound = std::round(upperCutoffmm / image->GetGeometry()->GetSpacing()[1])*image->GetDimension(0); - int upperBound = lowerBound + sizeRawScatteringData; - - for (int i = 0; i < lowerBound && i < imageSize; ++i) - { - rawOutputData[i] = 0; // everything than cannot be compensated shall be treated as garbage, here the upper 0.15mm - } - for (int i = lowerBound; i < upperBound && i < imageSize; ++i) - { - rawOutputData[i] = 1 / rawScatteringData[i-lowerBound]; - } - for (int i = upperBound; i < imageSize; ++i) - { - rawOutputData[i] = 0; // everything than cannot be compensated shall be treated as garbage - } - - - unsigned int dim[] = { image->GetDimension(0), image->GetDimension(1), 1 }; - curResizeImage->Initialize(mitk::MakeScalarPixelType(), 3, dim); - curResizeImage->SetGeometry(image->GetGeometry()); - curResizeImage->SetSlice(rawOutputData,0); - - delete[] rawOutputData; - - mitk::CastToItkImage(curResizeImage, m_FluenceCompResizedItk.at(m_ScatteringCoefficient)); - m_FluenceCompResized.at(m_ScatteringCoefficient) = mitk::GrabItkImageMemory(m_FluenceCompResizedItk.at(m_ScatteringCoefficient)); + if (m_CompensateForScattering) + { + auto curResizeImage = m_FluenceCompResized.at(m_ScatteringCoefficient); + bool doResampling = imagePA->GetDimension(0) != curResizeImage->GetDimension(0) || imagePA->GetDimension(1) != curResizeImage->GetDimension(1) + || imagePA->GetGeometry()->GetSpacing()[0] != curResizeImage->GetGeometry()->GetSpacing()[0] || imagePA->GetGeometry()->GetSpacing()[1] != curResizeImage->GetGeometry()->GetSpacing()[1]; + if (doResampling) + ResizeFluenceImage(imagePA->GetGeometry()->GetSpacing(), imagePA->GetDimensions()); - MITK_INFO << "Resized a fluence image."; - } - // actually apply the scattering compensation - imagePA = ApplyScatteringCompensation(imagePA, m_ScatteringCoefficient); - ImageReadAccessor inputReadAccessorPA(imagePA, imagePA->GetSliceData(0)); - image->SetSlice(inputReadAccessorPA.GetData(), 0); - } - } + imagePA = ApplyScatteringCompensation(imagePA, m_ScatteringCoefficient); } + } + if(imageUS.IsNotNull() && m_DataType == DataType::Beamformed_Short) + { + itkFloatImageType::Pointer itkImage; - //TODO: completely rewrite this mess - - imageVector[0] = Image::New(); - unsigned int dim[] = { image->GetDimension(0),image->GetDimension(1),1 }; - imageVector[0]->Initialize(image->GetPixelType(), 3, dim); - imageVector[0]->SetGeometry(image->GetGeometry()); + mitk::CastToItkImage(imageUS, itkImage); + imageUS = mitk::GrabItkImageMemory(itkImage); //thereby using float images + imageUS = CutOffTop(imageUS, 165); - imageVector[1] = Image::New(); - imageVector[1]->Initialize(image->GetPixelType(), 3, dim); - imageVector[1]->SetGeometry(image->GetGeometry()); + if (m_UseBModeFilter) + imageUS = ApplyBmodeFilter(imageUS, true); // the US Images get a logarithmic filter - ImageReadAccessor inputReadAccessorCopyPA(image, image->GetSliceData(0)); - imageVector[0]->SetSlice(inputReadAccessorCopyPA.GetData(), 0); - ImageReadAccessor inputReadAccessorCopyUS(image, image->GetSliceData(1)); - imageVector[1]->SetSlice(inputReadAccessorCopyUS.GetData(), 0); + if (m_VerticalSpacing) + imageUS = ResampleOutputVertical(imageUS, m_VerticalSpacing); } + + imageVector[0] = imagePA; + imageVector[1] = imageUS; } mitk::Image::Pointer mitk::USDiPhASImageSource::ApplyBmodeFilter(mitk::Image::Pointer image, bool useLogFilter) { // we use this seperate ApplyBmodeFilter Method for processing of two-dimensional images // 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::BModeImageFilter < itkFloatImageType, itkFloatImageType > BModeFilterType; BModeFilterType::Pointer bModeFilter = BModeFilterType::New(); // LogFilter typedef itk::PhotoacousticBModeImageFilter < itkFloatImageType, itkFloatImageType > PhotoacousticBModeImageFilter; PhotoacousticBModeImageFilter::Pointer photoacousticBModeFilter = PhotoacousticBModeImageFilter::New(); // No LogFilter itkFloatImageType::Pointer itkImage; itkFloatImageType::Pointer bmode; mitk::CastToItkImage(image, itkImage); if (useLogFilter) { bModeFilter->SetInput(itkImage); bModeFilter->SetDirection(1); bmode = bModeFilter->GetOutput(); } else { photoacousticBModeFilter->SetInput(itkImage); photoacousticBModeFilter->SetDirection(1); bmode = photoacousticBModeFilter->GetOutput(); } return mitk::GrabItkImageMemory(bmode); } mitk::Image::Pointer mitk::USDiPhASImageSource::CutOffTop(mitk::Image::Pointer image, int cutOffSize) { typedef itk::CropImageFilter < itkFloatImageType, itkFloatImageType > CutImageFilter; itkFloatImageType::SizeType cropSize; itkFloatImageType::Pointer itkImage; mitk::CastToItkImage(image, itkImage); cropSize[0] = 0; if(itkImage->GetLargestPossibleRegion().GetSize()[1] == 2048) cropSize[1] = cutOffSize; else cropSize[1] = 0; cropSize[2] = 0; CutImageFilter::Pointer cutOffFilter = CutImageFilter::New(); cutOffFilter->SetInput(itkImage); cutOffFilter->SetLowerBoundaryCropSize(cropSize); cutOffFilter->UpdateLargestPossibleRegion(); return mitk::GrabItkImageMemory(cutOffFilter->GetOutput()); } mitk::Image::Pointer mitk::USDiPhASImageSource::ResampleOutputVertical(mitk::Image::Pointer image, float verticalSpacing) { typedef itk::ResampleImageFilter < itkFloatImageType, itkFloatImageType > ResampleImageFilter; ResampleImageFilter::Pointer resampleImageFilter = ResampleImageFilter::New(); itkFloatImageType::Pointer itkImage; mitk::CastToItkImage(image, itkImage); itkFloatImageType::SpacingType outputSpacing; itkFloatImageType::SizeType inputSize = itkImage->GetLargestPossibleRegion().GetSize(); itkFloatImageType::SizeType outputSize = inputSize; outputSpacing[0] = itkImage->GetSpacing()[0] * (static_cast(inputSize[0]) / static_cast(outputSize[0])); outputSpacing[1] = verticalSpacing; 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()); } mitk::Image::Pointer mitk::USDiPhASImageSource::ApplyScatteringCompensation(mitk::Image::Pointer inputImage, int scattering) { 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::USDiPhASImageSource::ApplyResampling(mitk::Image::Pointer inputImage, mitk::Vector3D outputSpacing, unsigned int outputSize[3]) { typedef itk::ResampleImageFilter < itkFloatImageType, itkFloatImageType > ResampleImageFilter; ResampleImageFilter::Pointer resampleImageFilter = ResampleImageFilter::New(); itkFloatImageType::Pointer itkImage; mitk::CastToItkImage(inputImage, itkImage); itkFloatImageType::SpacingType outputSpacingItk; itkFloatImageType::SizeType inputSizeItk = itkImage->GetLargestPossibleRegion().GetSize(); itkFloatImageType::SizeType outputSizeItk = inputSizeItk; itkFloatImageType::SpacingType inputSpacing = itkImage->GetSpacing(); outputSizeItk[0] = outputSize[0]; outputSizeItk[1] = 10 * (inputSpacing[1] * inputSizeItk[1]) / (outputSpacing[1]); outputSizeItk[2] = 1; outputSpacingItk[0] = 0.996 * inputSpacing[0] * (static_cast(inputSizeItk[0]) / static_cast(outputSizeItk[0])); // TODO: find out why the spacing is not correct, so we need that factor; ?!?! outputSpacingItk[1] = inputSpacing[1] * (static_cast(inputSizeItk[1]) / static_cast(outputSizeItk[1])); outputSpacingItk[2] = outputSpacing[2]; typedef itk::IdentityTransform TransformType; resampleImageFilter->SetInput(itkImage); resampleImageFilter->SetSize(outputSizeItk); resampleImageFilter->SetOutputSpacing(outputSpacingItk); resampleImageFilter->SetTransform(TransformType::New()); resampleImageFilter->UpdateLargestPossibleRegion(); return mitk::GrabItkImageMemory(resampleImageFilter->GetOutput()); } mitk::Image::Pointer mitk::USDiPhASImageSource::MultiplyImage(mitk::Image::Pointer inputImage, double value) { typedef itk::MultiplyImageFilter MultiplyImageFilterType; itkFloatImageType::Pointer itkImage; mitk::CastToItkImage(inputImage, itkImage); MultiplyImageFilterType::Pointer multiplyFilter = MultiplyImageFilterType::New(); multiplyFilter->SetInput1(itkImage); multiplyFilter->SetConstant(value); return mitk::GrabItkImageMemory(multiplyFilter->GetOutput()); } void mitk::USDiPhASImageSource::ImageDataCallback( short* rfDataChannelData, int& channelDataChannelsPerDataset, int& channelDataSamplesPerChannel, int& channelDataTotalDatasets, short* rfDataArrayBeamformed, int& beamformedLines, int& beamformedSamples, int& beamformedTotalDatasets, unsigned char* imageData, int& imageWidth, int& imageHeight, int& imageBytesPerPixel, int& imageSetsTotal, double& timeStamp) { if (m_DataTypeModified) return; if (!m_PyroConnected) { m_Pyro = mitk::OphirPyro::New(); MITK_INFO << "[Pyro Debug] OpenConnection: " << m_Pyro->OpenConnection(); MITK_INFO << "[Pyro Debug] StartDataAcquisition: " << m_Pyro->StartDataAcquisition(); m_PyroConnected = true; } bool writeImage = ((m_DataType == DataType::Image_uChar) && (imageData != nullptr)) || ((m_DataType == DataType::Beamformed_Short) && (rfDataArrayBeamformed != nullptr)); if (writeImage) { - //get the timestamp we might save later on + unsigned int imageDimensions[3]; + //get the timestamp we will save later on m_CurrentImageTimestamp = std::chrono::high_resolution_clock::now().time_since_epoch().count(); - // create a new image and initialize it - mitk::Image::Pointer image = mitk::Image::New(); + // create new images and initialize them + mitk::Image::Pointer imageUS = mitk::Image::New(); + mitk::Image::Pointer imagePA = mitk::Image::New(); switch (m_DataType) { case DataType::Image_uChar: { - m_ImageDimensions[0] = imageWidth; - m_ImageDimensions[1] = imageHeight; - m_ImageDimensions[2] = imageSetsTotal; - image->Initialize(mitk::MakeScalarPixelType(), 3, m_ImageDimensions); + imageDimensions[0] = imageWidth; + imageDimensions[1] = imageHeight; + imageDimensions[2] = imageSetsTotal; + imageUS->Initialize(mitk::MakeScalarPixelType(), 3, imageDimensions); + imagePA->Initialize(mitk::MakeScalarPixelType(), 3, imageDimensions); + imageUS->GetGeometry()->SetSpacing(m_ImageSpacing); + imageUS->GetGeometry()->Modified(); break; } case DataType::Beamformed_Short: { - m_ImageDimensions[0] = beamformedLines; - m_ImageDimensions[1] = beamformedSamples; - m_ImageDimensions[2] = beamformedTotalDatasets; - image->Initialize(mitk::MakeScalarPixelType(), 3, m_ImageDimensions); + imageDimensions[0] = beamformedLines; + imageDimensions[1] = beamformedSamples; + imageDimensions[2] = beamformedTotalDatasets; + imageUS->Initialize(mitk::MakeScalarPixelType(), 3, imageDimensions); + imagePA->Initialize(mitk::MakeScalarPixelType(), 3, imageDimensions); + imagePA->GetGeometry()->SetSpacing(m_ImageSpacing); + imagePA->GetGeometry()->Modified(); break; } } - image->GetGeometry()->SetSpacing(m_ImageSpacing); - image->GetGeometry()->Modified(); // write the given buffer into the image switch (m_DataType) { case DataType::Image_uChar: { - for (unsigned char i = 0; i < imageSetsTotal; i++) { - image->SetSlice(&imageData[i*imageHeight*imageWidth], i); + if (m_Device->GetScanMode().beamformingAlgorithm == (int)Beamforming::Interleaved_OA_US) + { + imagePA->SetSlice(imageData); + imageUS->SetVolume(&imageData[imageHeight*imageWidth]); + } + else + { + imageUS->SetVolume(imageData); } break; } case DataType::Beamformed_Short: { short* flipme = new short[beamformedLines*beamformedSamples*beamformedTotalDatasets]; int pixelsPerImage = beamformedLines*beamformedSamples; for (unsigned char currentSet = 0; currentSet < beamformedTotalDatasets; currentSet++) { for (unsigned short sample = 0; sample < beamformedSamples; sample++) { for (unsigned short line = 0; line < beamformedLines; line++) { flipme[sample*beamformedLines + line + pixelsPerImage*currentSet] = rfDataArrayBeamformed[line*beamformedSamples + sample + pixelsPerImage*currentSet]; } } // the beamformed pa image is flipped by 90 degrees; we need to flip it manually } - - for (unsigned char i = 0; i < beamformedTotalDatasets; i++) { - image->SetSlice(&flipme[i*beamformedLines*beamformedSamples], i); - // set every image to a different slice - } - delete[] flipme; + if (m_Device->GetScanMode().beamformingAlgorithm == (int)Beamforming::Interleaved_OA_US) + { + imagePA->SetImportVolume(flipme, 0, 0, mitk::Image::ManageMemory); + imageUS->SetImportVolume(&flipme[beamformedLines*beamformedSamples], 0, 0, mitk::Image::ManageMemory); + } + else + { + imageUS->SetImportVolume(flipme, 0, 0, mitk::Image::ManageMemory); + } break; } } if (m_SavingSettings.saveRaw && m_CurrentlyRecording && rfDataChannelData != nullptr) { unsigned int dim[3]; dim[0] = channelDataChannelsPerDataset; dim[1] = channelDataSamplesPerChannel; dim[2] = 1; short offset = m_Device->GetScanMode().accumulation * 2048; short* noOffset = new short[channelDataChannelsPerDataset*channelDataSamplesPerChannel*channelDataTotalDatasets]; - for (unsigned char set = 0; set < 1; ++set)// channelDataTotalDatasets; ++set) // we ignore the raw US images for now + for (unsigned char set = 0; set < channelDataTotalDatasets; ++set) { for (unsigned short sam = 0; sam < channelDataSamplesPerChannel; ++sam) { for (unsigned short chan = 0; chan < channelDataChannelsPerDataset; ++chan) { noOffset[set*channelDataSamplesPerChannel*channelDataChannelsPerDataset + sam * channelDataChannelsPerDataset + chan] = rfDataChannelData[set*channelDataSamplesPerChannel*channelDataChannelsPerDataset + sam * channelDataChannelsPerDataset + chan] - offset; // this offset in the raw Images is given by the API... } } } + mitk::Image::Pointer rawImageUS = mitk::Image::New(); + mitk::Image::Pointer rawImagePA = mitk::Image::New(); - // save the raw images when recording - for (unsigned char i = 0; i < 1; ++i)// channelDataTotalDatasets; ++i) // we ignore the raw US images for now - { - mitk::Image::Pointer rawImage = mitk::Image::New(); - rawImage->Initialize(mitk::MakeScalarPixelType(), 3, dim); - - rawImage->SetSlice(&noOffset[i*channelDataChannelsPerDataset*channelDataSamplesPerChannel]); + mitk::Vector3D rawSpacing; + rawSpacing[0] = m_Device->GetScanMode().transducerPitchMeter * 1000; // save in mm + rawSpacing[1] = m_Device->GetScanMode().receivePhaseLengthSeconds / channelDataSamplesPerChannel * 1000000; // save in us + rawSpacing[2] = 1; - float& recordTime = m_Device->GetScanMode().receivePhaseLengthSeconds; - int& speedOfSound = m_Device->GetScanMode().averageSpeedOfSound; + rawImageUS->GetGeometry()->SetSpacing(rawSpacing); + rawImageUS->GetGeometry()->Modified(); + rawImagePA->GetGeometry()->SetSpacing(rawSpacing); + rawImagePA->GetGeometry()->Modified(); - mitk::Vector3D rawSpacing; - rawSpacing[0] = m_Device->GetScanMode().transducerPitchMeter * 1000; // save in mm - rawSpacing[1] = recordTime / channelDataSamplesPerChannel * 1000000; // save in us - rawSpacing[2] = 1; - - rawImage->GetGeometry()->SetSpacing(rawSpacing); - rawImage->GetGeometry()->Modified(); - - m_RawRecordedImages.push_back(rawImage); + if (m_Device->GetScanMode().beamformingAlgorithm == (int)Beamforming::Interleaved_OA_US) + { + rawImagePA->SetImportVolume(noOffset, 0, 0, mitk::Image::ManageMemory); + rawImageUS->SetImportVolume(&noOffset[channelDataChannelsPerDataset*channelDataSamplesPerChannel], 0, 0, mitk::Image::ManageMemory); } - - delete[] noOffset; + else + { + rawImageUS->SetImportVolume(noOffset, 0, 0, mitk::Image::ManageMemory); + } + // save the raw images when recording + m_RawRecordedImages.push_back(std::pair(rawImagePA, rawImageUS)); } - itk::Index<3> pixel = { { - (itk::Index<3>::IndexValueType)(image->GetDimension(0) / 2), - (itk::Index<3>::IndexValueType)(22.0/532.0*m_Device->GetScanMode().reconstructionSamplesPerLine), - 0 } }; //22/532*2048 = 84 - if (!m_Pyro->IsSyncDelaySet() &&(image->GetPixelValueByIndex(pixel) < -30)) // #MagicNumber + if (m_Device->GetScanMode().beamformingAlgorithm == (int)Beamforming::Interleaved_OA_US) { - MITK_INFO << "Setting SyncDelay now"; - m_Pyro->SetSyncDelay(m_CurrentImageTimestamp); + itk::Index<3> pixel = { { + (itk::Index<3>::IndexValueType)(imagePA->GetDimension(0) / 2), + (itk::Index<3>::IndexValueType)(22.0 / 532.0*m_Device->GetScanMode().reconstructionSamplesPerLine), + 0 } }; //22/532*2048 = 84 + if (!m_Pyro->IsSyncDelaySet() && (imagePA->GetPixelValueByIndex(pixel) < -30)) // #MagicNumber + { + MITK_INFO << "Setting SyncDelay now"; + m_Pyro->SetSyncDelay(m_CurrentImageTimestamp); + } } m_ImageTimestampBuffer[(m_LastWrittenImage + 1) % m_BufferSize] = m_CurrentImageTimestamp; - m_ImageBuffer[(m_LastWrittenImage + 1) % m_BufferSize] = image; + m_ImageBuffer[(m_LastWrittenImage + 1) % m_BufferSize] = std::pair(imagePA, imageUS); m_LastWrittenImage = (m_LastWrittenImage + 1) % m_BufferSize; // if the user decides to start recording, we feed the vector the generated images - if (m_CurrentlyRecording) { - for (unsigned char index = 0; index < image->GetDimension(2); ++index) - { - if (image->IsSliceSet(index)) - { - m_RecordedImages.push_back(Image::New()); - unsigned int dim[] = { image ->GetDimension(0), image->GetDimension(1), 1}; - m_RecordedImages.back()->Initialize(image->GetPixelType(), 3, dim); - m_RecordedImages.back()->SetGeometry(image->GetGeometry()); - - mitk::ImageReadAccessor inputReadAccessor(image, image->GetSliceData(index)); - m_RecordedImages.back()->SetSlice(inputReadAccessor.GetData(),0); - } - } - m_ImageTimestampRecord.push_back(m_CurrentImageTimestamp); - // save timestamps for each laser image! + if (m_CurrentlyRecording) + { + m_RecordedImages.push_back(std::pair(imagePA, imageUS)); + m_ImageTimestampRecord.push_back(m_CurrentImageTimestamp); // save timestamps for each PA image! } } } void mitk::USDiPhASImageSource::UpdateImageGeometry() { MITK_INFO << "Retreaving Image Geometry Information for Spacing..."; float& recordTime = m_Device->GetScanMode().receivePhaseLengthSeconds; int& speedOfSound = m_Device->GetScanMode().averageSpeedOfSound; float& pitch = m_Device->GetScanMode().reconstructedLinePitchMmOrAngleDegree; int& reconstructionLines = m_Device->GetScanMode().reconstructionLines; switch (m_DataType) { case DataType::Image_uChar : { int& imageWidth = m_Device->GetScanMode().imageWidth; int& imageHeight = m_Device->GetScanMode().imageHeight; m_ImageSpacing[0] = pitch * reconstructionLines / imageWidth; m_ImageSpacing[1] = recordTime * speedOfSound / 2 * 1000 / imageHeight; break; } case DataType::Beamformed_Short : { int& imageWidth = reconstructionLines; int& imageHeight = m_Device->GetScanMode().reconstructionSamplesPerLine; m_ImageSpacing[0] = pitch; m_ImageSpacing[1] = recordTime * speedOfSound / 2 * 1000 / imageHeight; break; } } m_ImageSpacing[2] = 1; MITK_INFO << "Retreaving Image Geometry Information for Spacing " << m_ImageSpacing[0] << " ... " << m_ImageSpacing[1] << " ... " << m_ImageSpacing[2] << " ...[DONE]"; } void mitk::USDiPhASImageSource::ModifyDataType(DataType dataT) { m_DataTypeModified = true; m_DataTypeNext = dataT; } void mitk::USDiPhASImageSource::ModifyUseBModeFilter(bool isSet) { m_UseBModeFilterModified = true; m_UseBModeFilterNext = isSet; } void mitk::USDiPhASImageSource::ModifyScatteringCoefficient(int coeff) { m_ScatteringCoefficientNext = coeff; m_ScatteringCoefficientModified = true; } void mitk::USDiPhASImageSource::ModifyCompensateForScattering(bool useIt) { m_CompensateForScatteringNext = useIt; m_CompensateForScatteringModified = true; } void mitk::USDiPhASImageSource::ModifyEnergyCompensation(bool compensate) { m_CompensateEnergyNext = compensate; m_CompensateEnergyModified = true; } void mitk::USDiPhASImageSource::SetDataType(DataType dataT) { if (dataT != m_DataType) { m_DataType = dataT; MITK_INFO << "Setting new DataType..." << dataT; switch (m_DataType) { case DataType::Image_uChar : MITK_INFO << "height: " << m_Device->GetScanMode().imageHeight << " width: " << m_Device->GetScanMode().imageWidth; break; case DataType::Beamformed_Short : MITK_INFO << "samples: " << m_Device->GetScanMode().reconstructionSamplesPerLine << " lines: " << m_Device->GetScanMode().reconstructionLines; break; } } } void mitk::USDiPhASImageSource::SetGUIOutput(std::function out) { USDiPhASImageSource::m_GUIOutput = out; m_StartTime = ((float)std::clock()) / CLOCKS_PER_SEC; //wait till the callback is available again m_UseGUIOutPut = false; } void mitk::USDiPhASImageSource::SetUseBModeFilter(bool isSet) { m_UseBModeFilter = isSet; } void mitk::USDiPhASImageSource::SetVerticalSpacing(float mm) { m_VerticalSpacingNext = mm; m_VerticalSpacingModified = true; } void mitk::USDiPhASImageSource::SetSavingSettings(SavingSettings settings) { m_SavingSettings = settings; } // this is just a little function to set the filenames below right inline void replaceAll(std::string& str, const std::string& from, const std::string& to) { if (from.empty()) return; size_t start_pos = 0; while ((start_pos = str.find(from, start_pos)) != std::string::npos) { str.replace(start_pos, from.length(), to); start_pos += to.length(); // In case 'to' contains 'from', like replacing 'x' with 'yx' } } void mitk::USDiPhASImageSource::SetRecordingStatus(bool record) { // start the recording process if (record) { m_RecordedImages.clear(); m_RawRecordedImages.clear(); // we make sure there are no leftovers m_ImageTimestampRecord.clear(); // also for the timestamps m_PixelValues.clear(); // aaaand for the pixel values if (m_SavingSettings.saveRaw) { m_Device->GetScanMode().transferChannelData = true; m_Device->UpdateScanmode(); // set the raw Data to be transfered } // tell the callback to start recording images m_CurrentlyRecording = true; } // save images, end recording, and clean up else { m_CurrentlyRecording = false; m_Device->GetScanMode().transferChannelData = false; // make sure raw Channel Data is not transferred anymore! m_Device->UpdateScanmode(); // get the time and date, put them into a nice string and create a folder for the images time_t time = std::time(nullptr); time_t* timeptr = &time; std::string currentDate = std::ctime(timeptr); replaceAll(currentDate, ":", "-"); currentDate.pop_back(); //std::string MakeFolder = "mkdir \"c:/DiPhASImageData/" + currentDate + "\""; //system(MakeFolder.c_str()); // initialize file paths and the images Image::Pointer PAImage = Image::New(); Image::Pointer USImage = Image::New(); std::string pathPA = "c:\\ImageData\\" + currentDate + "-" + "PAbeamformed" + ".nrrd"; std::string pathUS = "c:\\ImageData\\" + currentDate + "-" + "USImages" + ".nrrd"; std::string pathTS = "c:\\ImageData\\" + currentDate + "-" + "ts" + ".csv"; std::string pathS = "c:\\ImageData\\" + currentDate + "-" + "Settings" + ".txt"; // idon't forget the raw Images (if chosen to be saved) Image::Pointer PAImageRaw = Image::New(); Image::Pointer USImageRaw = Image::New(); std::string pathPARaw = "c:\\ImageData\\" + currentDate + "-" + "PAraw" + ".nrrd"; std::string pathUSRaw = "c:\\ImageData\\" + currentDate + "-" + "USImagesRaw" + ".nrrd"; if (m_Device->GetScanMode().beamformingAlgorithm == (int)Beamforming::Interleaved_OA_US) // save a PAImage if we used interleaved mode { // first, save the data, so the pyro does not aquire more unneccessary timestamps m_Pyro->SaveData(); // now order the images and save them // the beamformed ones... if (m_SavingSettings.saveBeamformed) { OrderImagesInterleaved(PAImage, USImage, m_RecordedImages, false); mitk::IOUtil::Save(USImage, pathUS); mitk::IOUtil::Save(PAImage, pathPA); } // ...and the raw images if (m_SavingSettings.saveRaw) { OrderImagesInterleaved(PAImageRaw, USImageRaw, m_RawRecordedImages, true); // mitk::IOUtil::Save(USImageRaw, pathUSRaw); mitk::IOUtil::Save(PAImageRaw, pathPARaw); } // read the pixelvalues of the enveloped images at this position + if (m_RecordedImages.at(0).first != nullptr && m_RecordedImages.at(0).first.IsNotNull()) + { + itk::Index<3> pixel = { { + (itk::Index<3>::IndexValueType)(m_RecordedImages.at(0).first->GetDimension(0) / 2), + (itk::Index<3>::IndexValueType)(22.0 / 532.0*m_Device->GetScanMode().reconstructionSamplesPerLine), + 0 } }; //22/532*2048 = 84 - itk::Index<3> pixel = { { - (itk::Index<3>::IndexValueType)(m_RecordedImages.at(0)->GetDimension(0) / 2), - (itk::Index<3>::IndexValueType)(22.0 / 532.0*m_Device->GetScanMode().reconstructionSamplesPerLine), - 0 } }; //22/532*2048 = 84 - - GetPixelValues(pixel, m_PixelValues); // write the Pixelvalues to m_PixelValues + GetPixelValues(pixel, m_PixelValues); // write the Pixelvalues to m_PixelValues + } // save the timestamps! ofstream timestampFile; timestampFile.open(pathTS); timestampFile << ",timestamp,pixelvalue"; // write the header for (int index = 0; index < m_ImageTimestampRecord.size(); ++index) { timestampFile << "\n" << index << "," << m_ImageTimestampRecord.at(index) << "," << m_PixelValues.at(index); } timestampFile.close(); //save the settings! ofstream settingsFile; settingsFile.open(pathS); auto& sM = m_Device->GetScanMode(); settingsFile << "[General Parameters]\n"; settingsFile << "Scan Depth [mm] = " << sM.receivePhaseLengthSeconds * sM.averageSpeedOfSound / 2 * 1000 << "\n"; settingsFile << "Speed of Sound [m/s] = " << sM.averageSpeedOfSound << "\n"; settingsFile << "Excitation Frequency [MHz] = " << sM.transducerFrequencyHz/1000000 << "\n"; settingsFile << "Voltage [V] = " << sM.voltageV << "\n"; settingsFile << "TGC min = " << (int)sM.tgcdB[0] << " max = " << (int)sM.tgcdB[7] << "\n"; settingsFile << "[Beamforming Parameters]\n"; settingsFile << "Reconstructed Lines = " << sM.reconstructionLines << "\n"; settingsFile << "Samples per Line = " << sM.reconstructionSamplesPerLine << "\n"; settingsFile.close(); } else if (m_Device->GetScanMode().beamformingAlgorithm == (int)Beamforming::PlaneWaveCompound) // save no PAImage if we used US only mode { OrderImagesUltrasound(USImage, m_RecordedImages); mitk::IOUtil::Save(USImage, pathUS); } m_PixelValues.clear(); m_RawRecordedImages.clear(); // clean up the pixel values m_RecordedImages.clear(); // clean up the images m_ImageTimestampRecord.clear(); // clean up the timestamps } } void mitk::USDiPhASImageSource::GetPixelValues(itk::Index<3> pixel, std::vector& values) { unsigned int events = 2; for (int index = 0; index < m_RecordedImages.size(); index += events) // omit sound images { - Image::Pointer image = m_RecordedImages.at(index); - image = ApplyBmodeFilter(image); - values.push_back(image.GetPointer()->GetPixelValueByIndex(pixel)); + Image::Pointer image = m_RecordedImages.at(index).first; + if (image != nullptr && image.IsNotNull()) + { + image = ApplyBmodeFilter(image); + values.push_back(image.GetPointer()->GetPixelValueByIndex(pixel)); + } } } -void mitk::USDiPhASImageSource::OrderImagesInterleaved(Image::Pointer PAImage, Image::Pointer USImage, std::vector recordedList, bool raw) +void mitk::USDiPhASImageSource::OrderImagesInterleaved(Image::Pointer PAImage, Image::Pointer USImage, std::vector> recordedList, bool raw) { unsigned int width = 32; unsigned int height = 32; - unsigned int events = m_Device->GetScanMode().transmitEventsCount + 1; // the PA event is not included in the transmitEvents, so we add 1 here + unsigned int events = m_Device->GetScanMode().transmitEventsCount; if (!raw) - events = 2; // the beamformed image array contains only the resulting image of multiple events + events = 1; // the beamformed image array contains only the resulting image of multiple events if (raw) { - width = recordedList.at(0)->GetDimension(0); - height = recordedList.at(0)->GetDimension(1); + width = recordedList.at(0).first->GetDimension(0); + height = recordedList.at(0).first->GetDimension(1); } else if (m_DataType == DataType::Beamformed_Short) { width = m_Device->GetScanMode().reconstructionLines; height = m_Device->GetScanMode().reconstructionSamplesPerLine; } else if (m_DataType == DataType::Image_uChar) { width = m_Device->GetScanMode().imageWidth; height = m_Device->GetScanMode().imageHeight; } - unsigned int dimLaser[] = { (unsigned int)width, (unsigned int)height, (unsigned int)(recordedList.size() / events)}; - unsigned int dimSound[] = { (unsigned int)width, (unsigned int)height, (unsigned int)(recordedList.size() / events * (events-1))}; + unsigned int dimLaser[] = { width, height, (unsigned int)recordedList.size()}; + unsigned int dimSound[] = { width, height, (unsigned int)(recordedList.size() * events)}; - PAImage->Initialize(recordedList.back()->GetPixelType(), 3, dimLaser); - PAImage->SetGeometry(recordedList.back()->GetGeometry()); - USImage->Initialize(recordedList.back()->GetPixelType(), 3, dimSound); - USImage->SetGeometry(recordedList.back()->GetGeometry()); + PAImage->Initialize(recordedList.back().first->GetPixelType(), 3, dimLaser); + PAImage->SetSpacing(recordedList.back().first->GetGeometry()->GetSpacing()); + USImage->Initialize(recordedList.back().first->GetPixelType(), 3, dimSound); + USImage->SetSpacing(recordedList.back().first->GetGeometry()->GetSpacing()); for (int index = 0; index < recordedList.size(); ++index) { - mitk::ImageReadAccessor inputReadAccessor(recordedList.at(index)); + mitk::ImageReadAccessor inputReadAccessorPA(recordedList.at(index).first); + PAImage->SetSlice(inputReadAccessorPA.GetData(), index); - if (index % events == 0) - { - PAImage->SetSlice(inputReadAccessor.GetData(), index / events); - } - else + for (unsigned int i = 0; i < events; ++i) { - if(!raw) - USImage->SetSlice(inputReadAccessor.GetData(), ((index - (index % events)) / events) + (index % events)-1); + mitk::ImageReadAccessor inputReadAccessorUS(recordedList.at(index).second, recordedList.at(index).second->GetSliceData(i)); + USImage->SetSlice(inputReadAccessorUS.GetData(), index + i); } } } -void mitk::USDiPhASImageSource::OrderImagesUltrasound(Image::Pointer USImage, std::vector recordedList) +void mitk::USDiPhASImageSource::OrderImagesUltrasound(Image::Pointer USImage, std::vector> recordedList) { unsigned int width = 32; unsigned int height = 32; unsigned int events = m_Device->GetScanMode().transmitEventsCount; if (m_DataType == DataType::Beamformed_Short) { width = (unsigned int)m_Device->GetScanMode().reconstructionLines; height = (unsigned int)m_Device->GetScanMode().reconstructionSamplesPerLine; } else if (m_DataType == DataType::Image_uChar) { width = (unsigned int)m_Device->GetScanMode().imageWidth; height = (unsigned int)m_Device->GetScanMode().imageHeight; } - unsigned int dimSound[] = { (unsigned int)width, (unsigned int)height, (unsigned int)recordedList.size()}; + unsigned int dimSound[] = { width, height, (unsigned int)(recordedList.size() * events) }; - USImage->Initialize(recordedList.back()->GetPixelType(), 3, dimSound); - USImage->SetGeometry(recordedList.back()->GetGeometry()); + USImage->Initialize(recordedList.back().second->GetPixelType(), 3, dimSound); + USImage->SetSpacing(recordedList.back().second->GetGeometry()->GetSpacing()); for (int index = 0; index < recordedList.size(); ++index) { - mitk::ImageReadAccessor inputReadAccessor(recordedList.at(index)); - USImage->SetSlice(inputReadAccessor.GetData(), index); + for (unsigned int i = 0; i < events; ++i) + { + mitk::ImageReadAccessor inputReadAccessorUS(recordedList.at(index).second, recordedList.at(index).second->GetSliceData(i)); + USImage->SetSlice(inputReadAccessorUS.GetData(), index + i); + } } } \ No newline at end of file diff --git a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASImageSource.h b/Modules/US/USHardwareDiPhAS/mitkUSDiPhASImageSource.h index 54ac576ffd..ea9c4f24e8 100644 --- a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASImageSource.h +++ b/Modules/US/USHardwareDiPhAS/mitkUSDiPhASImageSource.h @@ -1,193 +1,198 @@ /*=================================================================== 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 MITKUSDiPhASImageSource_H_HEADER_INCLUDED_ #define MITKUSDiPhASImageSource_H_HEADER_INCLUDED_ #include "mitkUSImageSource.h" #include "mitkUSDiPhASCustomControls.h" #include "Framework.IBMT.US.CWrapper.h" #include "mitkImageReadAccessor.h" #include "itkFastMutexLock.h" #include #include #include #include #include #include #include #include namespace mitk { class USDiPhASDevice; /** * \brief Implementation of mitk::USImageSource for DiPhAS API devices. * The method mitk::USImageSource::GetNextRawImage() is implemented for * getting images from the DiPhAS API. * * The image data is given to this class from the DiPhAS API by calling * a callback method that writes the image data to an mitk::image */ class USDiPhASImageSource : public USImageSource { public: mitkClassMacro(USDiPhASImageSource, USImageSource); mitkNewMacro1Param(Self, mitk::USDiPhASDevice*); itkCloneMacro(Self); typedef itk::Image< float, 3 > itkFloatImageType; typedef mitk::USDiPhASDeviceCustomControls::DataType DataType; typedef mitk::USDiPhASDeviceCustomControls::SavingSettings SavingSettings; /** * Implementation of the superclass method. Returns the pointer * to the mitk::Image filled by DiPhAS API callback. */ virtual void GetNextRawImage( std::vector& ) override; /** * The API calls this function to pass the image data to the * user; here the m_Image is updated */ void mitk::USDiPhASImageSource::ImageDataCallback( short* rfDataChannelData, int& channelDataChannelsPerDataset, int& channelDataSamplesPerChannel, int& channelDataTotalDatasets, short* rfDataArrayBeamformed, int& beamformedLines, int& beamformedSamples, int& beamformedTotalDatasets, unsigned char* imageData, int& imageWidth, int& imageHeight, int& imagePixelFormat, int& imageSetsTotal, double& timeStamp); void SetGUIOutput(std::function out); /** This starts or ends the recording session*/ void SetRecordingStatus(bool record); void SetSavingSettings(SavingSettings settings); void SetVerticalSpacing(float mm); void ModifyDataType(DataType dataT); void ModifyUseBModeFilter(bool isSet); void ModifyScatteringCoefficient(int coeff); void ModifyCompensateForScattering(bool useIt); void ModifyEnergyCompensation(bool compensate); /** * Sets the spacing used in the image based on the informations of the ScanMode in USDiPhAS Device */ void UpdateImageGeometry(); protected: void SetDataType(DataType dataT); void SetUseBModeFilter(bool isSet); + void CheckModifiedVariables(); + void ResizeFluenceImage(mitk::Vector3D spacing, unsigned int* dimensions); + USDiPhASImageSource(mitk::USDiPhASDevice* device); virtual ~USDiPhASImageSource( ); /** This vector holds all the images we record, if recording is set to active. */ - std::vector m_RecordedImages; - std::vector m_RawRecordedImages; - std::vector m_ImageTimestampRecord; - std::vector m_ImageTimestampBuffer; + std::vector> m_RecordedImages; // first image US, second image PA + std::vector> m_RawRecordedImages; + std::vector m_ImageTimestampRecord; // stores all timestamps since recording started + + std::vector> m_ImageBuffer; // first image US, second image PA + std::vector m_ImageTimestampBuffer; // stores all timestamps since recording started + long long m_CurrentImageTimestamp; bool m_CurrentlyRecording; + mitk::OphirPyro::Pointer m_Pyro; bool m_PyroConnected; std::vector m_FluenceCompOriginal; std::vector m_FluenceCompResized; std::vector::Pointer> m_FluenceCompResizedItk; - std::vector m_ImageBuffer; int m_LastWrittenImage; int m_BufferSize; - unsigned int m_ImageDimensions[3]; mitk::Vector3D m_ImageSpacing; mitk::Image::Pointer ApplyBmodeFilter(mitk::Image::Pointer image, bool useLogFilter = false); mitk::Image::Pointer CutOffTop(mitk::Image::Pointer image, int cutOffSize = 165); mitk::Image::Pointer ResampleOutputVertical(mitk::Image::Pointer image, float verticalSpacing = 0.1); mitk::Image::Pointer ApplyScatteringCompensation(mitk::Image::Pointer inputImage, int scatteringCoefficient); mitk::Image::Pointer ApplyResampling(mitk::Image::Pointer inputImage, mitk::Vector3D outputSpacing, unsigned int outputSize[3]); mitk::Image::Pointer MultiplyImage(mitk::Image::Pointer inputImage, double value); - void OrderImagesInterleaved(Image::Pointer PAImage, Image::Pointer USImage, std::vector recordedList, bool raw); - void OrderImagesUltrasound(Image::Pointer USImage, std::vector recordedList); + void OrderImagesInterleaved(Image::Pointer PAImage, Image::Pointer USImage, std::vector> recordedList, bool raw); + void OrderImagesUltrasound(Image::Pointer USImage, std::vector> recordedList); void GetPixelValues(itk::Index<3> pixel, std::vector& values); float GetPixelValue(itk::Index<3> pixel); std::vector m_PixelValues; mitk::USDiPhASDevice* m_Device; /** This is a callback to pass text data to the GUI. */ std::function m_GUIOutput; /** * Variables for management of current state. */ SavingSettings m_SavingSettings; float m_StartTime; bool m_UseGUIOutPut; BeamformerStateInfoNative m_BeamformerInfos; bool m_UseBModeFilter; bool m_DataTypeModified; DataType m_DataTypeNext; bool m_UseBModeFilterModified; bool m_UseBModeFilterNext; float m_VerticalSpacing; float m_VerticalSpacingNext; bool m_VerticalSpacingModified; int m_ScatteringCoefficient; int m_ScatteringCoefficientNext; bool m_ScatteringCoefficientModified; bool m_CompensateForScattering; bool m_CompensateForScatteringNext; bool m_CompensateForScatteringModified; bool m_CompensateEnergy; bool m_CompensateEnergyNext; bool m_CompensateEnergyModified; DataType m_DataType; }; } // namespace mitk #endif // MITKUSDiPhASImageSource_H