diff --git a/Modules/PhotoacousticsAlgorithms/mitkPhotoacousticImage.cpp b/Modules/PhotoacousticsAlgorithms/mitkPhotoacousticImage.cpp index 8745b81f28..b0dafea15f 100644 --- a/Modules/PhotoacousticsAlgorithms/mitkPhotoacousticImage.cpp +++ b/Modules/PhotoacousticsAlgorithms/mitkPhotoacousticImage.cpp @@ -1,587 +1,603 @@ /*=================================================================== 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 "mitkImageCast.h" #include "mitkITKImageImport.h" #include "mitkPhotoacousticBeamformingFilter.h" #include #include // itk dependencies #include "itkImage.h" #include "itkResampleImageFilter.h" #include "itkCastImageFilter.h" #include "itkCropImageFilter.h" #include "itkRescaleIntensityImageFilter.h" #include "itkIntensityWindowingImageFilter.h" #include #include "itkMultiplyImageFilter.h" #include "itkBSplineInterpolateImageFunction.h" #include // needed itk image filters #include "mitkITKImageImport.h" #include "itkFFTShiftImageFilter.h" #include "itkMultiplyImageFilter.h" #include "itkComplexToModulusImageFilter.h" #include #include "itkFFT1DComplexConjugateToRealImageFilter.h" #include "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, bool UseLogFilter, float resampleSpacing) { // 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::Image< float, 3 > itkFloatImageType; 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] * (static_cast(inputSize[0]) / static_cast(outputSize[0])); outputSpacing[1] = resampleSpacing; outputSpacing[2] = itkImage->GetSpacing()[2]; outputSize[1] = inputSize[1] * itkImage->GetSpacing()[1] / outputSpacing[1]; typedef itk::IdentityTransform TransformType; resampleImageFilter->SetInput(bmode); resampleImageFilter->SetSize(outputSize); resampleImageFilter->SetOutputSpacing(outputSpacing); resampleImageFilter->SetTransform(TransformType::New()); resampleImageFilter->UpdateLargestPossibleRegion(); return mitk::GrabItkImageMemory(resampleImageFilter->GetOutput()); } /*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 inputSpacing = itkImage->GetSpacing(); 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) - above - below, maxSlice - 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) { // crop the image // set the Maximum Size of the image to 4096 unsigned short lowerCutoff = (4096 + cutoff) < inputImage->GetDimension(1) ? inputImage->GetDimension(1) - 4096 : 0; config.RecordTime = config.RecordTime - (cutoff + lowerCutoff) / 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; } // 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) { - if (data->GetDimension(1) % 2 != 0) + MITK_INFO << "here"; + bool powerOfTwo = false; + int finalPower = 0; + for (int i = 1; pow(2, i) <= data->GetDimension(1); ++i) { - int CropBounds[2] = { 0, data->GetDimension(2) - 1 }; - data = ApplyCropping(data, 1, 0, 0, 0, CropBounds[0], CropBounds[1]); - //for the itk filter to work we make sure the 2nd dimension is a multiple of 2 + MITK_INFO << "here"; + finalPower = i; + if (pow(2, i) == data->GetDimension(1)) + { + powerOfTwo = true; + } + } + MITK_INFO << "here"; + if (!powerOfTwo) + { + unsigned int dim[2] = { data->GetDimension(0), pow(2,finalPower+1)}; + MITK_INFO << "there"; + 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 (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 (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 (int line = 1; line < reference->GetDimension(0); ++line) { for (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