diff --git a/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticImage.h b/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticImage.h index 504fdc1090..404c814412 100644 --- a/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticImage.h +++ b/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticImage.h @@ -1,125 +1,129 @@ /*=================================================================== 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); + mitk::Image::Pointer BandpassFilter(mitk::Image::Pointer data, float recordTime, + float BPHighPass, float BPLowPass, + float alphaHighPass, float alphaLowPass); protected: PhotoacousticImage(); ~PhotoacousticImage() override; /** \brief For performance reasons, an instance of the Beamforming filter is initialized as soon as possible and kept for all further uses. */ mitk::BeamformingFilter::Pointer m_BeamformingFilter; /** \brief Function that creates a Tukey function for the bandpass */ - itk::Image::Pointer BPFunction(mitk::Image::Pointer reference, int cutoffFrequencyPixelHighPass, int cutoffFrequencyPixelLowPass, float alpha); + itk::Image::Pointer BPFunction(mitk::Image::Pointer reference, + int cutoffFrequencyPixelHighPass, int cutoffFrequencyPixelLowPass, + float alphaHighPass, float alphaLowPass); }; } // namespace mitk #endif /* mitkPhotoacousticImage_H_HEADER_INCLUDED */ diff --git a/Modules/PhotoacousticsAlgorithms/source/mitkPhotoacousticImage.cpp b/Modules/PhotoacousticsAlgorithms/source/mitkPhotoacousticImage.cpp index d4961e2260..41c3c3b0f5 100644 --- a/Modules/PhotoacousticsAlgorithms/source/mitkPhotoacousticImage.cpp +++ b/Modules/PhotoacousticsAlgorithms/source/mitkPhotoacousticImage.cpp @@ -1,539 +1,517 @@ /*=================================================================== 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 "mitkPhotoacousticImage.h" #include "../ITKFilter/ITKUltrasound/itkBModeImageFilter.h" #include "../ITKFilter/itkPhotoacousticBModeImageFilter.h" #include "mitkImageCast.h" #include "mitkITKImageImport.h" #include "mitkPhotoacousticBeamformingFilter.h" #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 "../ITKFilter/ITKUltrasound/itkFFT1DComplexConjugateToRealImageFilter.h" #include "../ITKFilter/ITKUltrasound/itkFFT1DRealToComplexConjugateImageFilter.h" 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 UseGPU, bool UseLogFilter, float resampleSpacing) { // the image needs to be of floating point type for the envelope filter to work; the casting is done automatically by the CastToItkImage typedef itk::Image< float, 3 > itkFloatImageType; typedef itk::IdentityTransform TransformType; if (method == BModeMethod::Abs) { mitk::Image::Pointer input; mitk::Image::Pointer out; if (inputImage->GetPixelType().GetTypeAsString() == "scalar (float)" || inputImage->GetPixelType().GetTypeAsString() == " (float)") input = inputImage; else input = ApplyCropping(inputImage, 0, 0, 0, 0, 0, inputImage->GetDimension(2) - 1); if (!UseGPU) { PhotoacousticBModeFilter::Pointer filter = PhotoacousticBModeFilter::New(); filter->SetParameters(UseLogFilter); filter->SetInput(input); filter->Update(); out = filter->GetOutput(); if (resampleSpacing == 0) return out; } #ifdef PHOTOACOUSTICS_USE_GPU else { PhotoacousticOCLBModeFilter::Pointer filter = PhotoacousticOCLBModeFilter::New(); filter->SetParameters(UseLogFilter); filter->SetInput(input); filter->Update(); out = filter->GetOutput(); if (resampleSpacing == 0) return out; } #endif typedef itk::ResampleImageFilter < itkFloatImageType, itkFloatImageType > ResampleImageFilter; ResampleImageFilter::Pointer resampleImageFilter = ResampleImageFilter::New(); itkFloatImageType::Pointer itkImage; mitk::CastToItkImage(out, itkImage); itkFloatImageType::SpacingType outputSpacing; itkFloatImageType::SizeType inputSize = itkImage->GetLargestPossibleRegion().GetSize(); itkFloatImageType::SizeType outputSize = inputSize; outputSpacing[0] = itkImage->GetSpacing()[0]; outputSpacing[1] = resampleSpacing; outputSpacing[2] = itkImage->GetSpacing()[2]; outputSize[1] = inputSize[1] * itkImage->GetSpacing()[1] / outputSpacing[1]; typedef itk::IdentityTransform TransformType; resampleImageFilter->SetInput(itkImage); resampleImageFilter->SetSize(outputSize); resampleImageFilter->SetOutputSpacing(outputSpacing); resampleImageFilter->SetTransform(TransformType::New()); resampleImageFilter->UpdateLargestPossibleRegion(); return mitk::GrabItkImageMemory(resampleImageFilter->GetOutput()); } else if (method == BModeMethod::EnvelopeDetection) { typedef itk::BModeImageFilter < itkFloatImageType, itkFloatImageType > BModeFilterType; BModeFilterType::Pointer bModeFilter = BModeFilterType::New(); // LogFilter typedef itk::PhotoacousticBModeImageFilter < itkFloatImageType, itkFloatImageType > PhotoacousticBModeImageFilter; PhotoacousticBModeImageFilter::Pointer photoacousticBModeFilter = PhotoacousticBModeImageFilter::New(); // No LogFilter typedef itk::ResampleImageFilter < itkFloatImageType, itkFloatImageType > ResampleImageFilter; ResampleImageFilter::Pointer resampleImageFilter = ResampleImageFilter::New(); itkFloatImageType::Pointer itkImage; mitk::CastToItkImage(inputImage, itkImage); itkFloatImageType::Pointer bmode; if (UseLogFilter) { bModeFilter->SetInput(itkImage); bModeFilter->SetDirection(1); bmode = bModeFilter->GetOutput(); } else { photoacousticBModeFilter->SetInput(itkImage); photoacousticBModeFilter->SetDirection(1); bmode = photoacousticBModeFilter->GetOutput(); } // resampleSpacing == 0 means: do no resampling if (resampleSpacing == 0) { return mitk::GrabItkImageMemory(bmode); } itkFloatImageType::SpacingType outputSpacing; itkFloatImageType::SizeType inputSize = itkImage->GetLargestPossibleRegion().GetSize(); itkFloatImageType::SizeType outputSize = inputSize; outputSpacing[0] = itkImage->GetSpacing()[0]; outputSpacing[1] = resampleSpacing; outputSpacing[2] = itkImage->GetSpacing()[2]; outputSize[1] = inputSize[1] * itkImage->GetSpacing()[1] / outputSpacing[1]; resampleImageFilter->SetInput(bmode); resampleImageFilter->SetSize(outputSize); resampleImageFilter->SetOutputSpacing(outputSpacing); resampleImageFilter->SetTransform(TransformType::New()); resampleImageFilter->UpdateLargestPossibleRegion(); return mitk::GrabItkImageMemory(resampleImageFilter->GetOutput()); } return nullptr; } /*mitk::Image::Pointer mitk::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 float, short, double are used at all. if (inputImage->GetPixelType().GetTypeAsString() == "scalar (float)" || inputImage->GetPixelType().GetTypeAsString() == " (float)") { // copy the data into the cropped image for (unsigned short sl = 0; sl < outputDim[2]; ++sl) { for (unsigned short l = 0; l < outputDim[0]; ++l) { for (unsigned short s = 0; s < outputDim[1]; ++s) { outputData[l + s*(unsigned short)outputDim[0] + sl*outputDim[0] * outputDim[1]] = (float)((float*)inputData)[(l + left) + (s + above)*(unsigned short)inputDim[0] + (sl + minSlice)*inputDim[0] * inputDim[1]]; } } } } else if (inputImage->GetPixelType().GetTypeAsString() == "scalar (short)" || inputImage->GetPixelType().GetTypeAsString() == " (short)") { // copy the data to the cropped image for (unsigned short sl = 0; sl < outputDim[2]; ++sl) { for (unsigned short l = 0; l < outputDim[0]; ++l) { for (unsigned short s = 0; s < outputDim[1]; ++s) { outputData[l + s*(unsigned short)outputDim[0] + sl*outputDim[0] * outputDim[1]] = (float)((short*)inputData)[(l + left) + (s + above)*(unsigned short)inputDim[0] + (sl + minSlice)*inputDim[0] * inputDim[1]]; } } } } else if (inputImage->GetPixelType().GetTypeAsString() == "scalar (double)" || inputImage->GetPixelType().GetTypeAsString() == " (double)") { // copy the data to the cropped image for (unsigned short sl = 0; sl < outputDim[2]; ++sl) { for (unsigned short l = 0; l < outputDim[0]; ++l) { for (unsigned short s = 0; s < outputDim[1]; ++s) { outputData[l + s*(unsigned short)outputDim[0] + sl*outputDim[0] * outputDim[1]] = (float)((double*)inputData)[(l + left) + (s + above)*(unsigned short)inputDim[0] + (sl + minSlice)*inputDim[0] * inputDim[1]]; } } } } else { MITK_INFO << "Could not determine pixel type"; } mitk::Image::Pointer output = mitk::Image::New(); output->Initialize(mitk::MakeScalarPixelType(), 3, outputDim); output->SetSpacing(inputImage->GetGeometry()->GetSpacing()); output->SetImportVolume(outputData, 0, 0, mitk::Image::ReferenceMemory); return output; } mitk::Image::Pointer mitk::PhotoacousticImage::ApplyBeamforming(mitk::Image::Pointer inputImage, BeamformingSettings config, std::string& message, std::function progressHandle) { Image::Pointer processedImage = inputImage; if (inputImage->GetDimension() != 3) { processedImage->Initialize(mitk::MakeScalarPixelType(), 3, inputImage->GetDimensions()); processedImage->SetSpacing(inputImage->GetGeometry()->GetSpacing()); mitk::ImageReadAccessor copy(inputImage); processedImage->SetImportVolume(copy.GetData()); } 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]); config.inputDim[0] = processedImage->GetDimension(0); config.inputDim[1] = processedImage->GetDimension(1); config.inputDim[2] = processedImage->GetDimension(2); // perform the beamforming m_BeamformingFilter->SetInput(processedImage); m_BeamformingFilter->Configure(config); m_BeamformingFilter->SetProgressHandle(progressHandle); m_BeamformingFilter->UpdateLargestPossibleRegion(); 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) +mitk::Image::Pointer mitk::PhotoacousticImage::BandpassFilter(mitk::Image::Pointer data, float recordTime, + float BPHighPass, float BPLowPass, + float alphaHighPass, float alphaLowPass) { bool powerOfTwo = false; int finalPower = 0; for (int i = 1; pow(2, i) <= data->GetDimension(1); ++i) { finalPower = i; if (pow(2, i) == data->GetDimension(1)) { powerOfTwo = true; } } if (!powerOfTwo) { unsigned int dim[2] = { data->GetDimension(0), (unsigned int)pow(2,finalPower+1)}; data = ApplyResampling(data, dim); } MITK_INFO << data->GetDimension(0); // do a fourier transform, multiply with an appropriate window for the filter, and transform back typedef float PixelType; typedef itk::Image< PixelType, 3 > RealImageType; RealImageType::Pointer image; mitk::CastToItkImage(data, image); typedef itk::FFT1DRealToComplexConjugateImageFilter ForwardFFTFilterType; typedef ForwardFFTFilterType::OutputImageType ComplexImageType; ForwardFFTFilterType::Pointer forwardFFTFilter = ForwardFFTFilterType::New(); forwardFFTFilter->SetInput(image); forwardFFTFilter->SetDirection(1); try { forwardFFTFilter->UpdateOutputInformation(); } catch (itk::ExceptionObject & error) { std::cerr << "Error: " << error << std::endl; MITK_WARN << "Bandpass could not be applied"; return data; } float singleVoxel = 1 / (recordTime / data->GetDimension(1)) / 2 / 1000; float cutoffPixelHighPass = std::min(BPHighPass / singleVoxel, (float)data->GetDimension(1) / 2); float cutoffPixelLowPass = std::min(BPLowPass / singleVoxel, (float)data->GetDimension(1) / 2 - cutoffPixelHighPass); - RealImageType::Pointer fftMultiplicator = BPFunction(data, cutoffPixelHighPass, cutoffPixelLowPass, alpha); + RealImageType::Pointer fftMultiplicator = BPFunction(data, cutoffPixelHighPass, cutoffPixelLowPass, alphaHighPass, alphaLowPass); typedef itk::MultiplyImageFilter< ComplexImageType, RealImageType, ComplexImageType > MultiplyFilterType; MultiplyFilterType::Pointer multiplyFilter = MultiplyFilterType::New(); multiplyFilter->SetInput1(forwardFFTFilter->GetOutput()); multiplyFilter->SetInput2(fftMultiplicator); /*itk::ComplexToModulusImageFilter::Pointer toReal = itk::ComplexToModulusImageFilter::New(); toReal->SetInput(forwardFFTFilter->GetOutput()); return GrabItkImageMemory(toReal->GetOutput()); return GrabItkImageMemory(fftMultiplicator); *///DEBUG typedef itk::FFT1DComplexConjugateToRealImageFilter< ComplexImageType, RealImageType > InverseFilterType; InverseFilterType::Pointer inverseFFTFilter = InverseFilterType::New(); inverseFFTFilter->SetInput(multiplyFilter->GetOutput()); inverseFFTFilter->SetDirection(1); return GrabItkImageMemory(inverseFFTFilter->GetOutput()); } -itk::Image::Pointer mitk::PhotoacousticImage::BPFunction(mitk::Image::Pointer reference, int cutoffFrequencyPixelHighPass, int cutoffFrequencyPixelLowPass, float alpha) +itk::Image::Pointer mitk::PhotoacousticImage::BPFunction(mitk::Image::Pointer reference, + int cutoffFrequencyPixelHighPass, + int cutoffFrequencyPixelLowPass, + float alphaHighPass, float alphaLowPass) { 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; + float width = reference->GetDimension(1) / 2.0 - (float)cutoffFrequencyPixelHighPass - (float)cutoffFrequencyPixelLowPass; + float center = (float)cutoffFrequencyPixelHighPass / 2.0 + width / 2.0; for (unsigned int n = 0; n < reference->GetDimension(1); ++n) { imageData[reference->GetDimension(0)*n] = 0; } - if (alpha < 0.00001) + for (int n = 0; n < width; ++n) { - for (int n = 0; n < width; ++n) + imageData[reference->GetDimension(0)*n] = 1; + if (n <= (alphaHighPass*(width - 1)) / 2.0) { - if (n <= (alpha*(width - 1)) / 2) - { - imageData[reference->GetDimension(0)*(int)(n + center - (width / 2))] = (1 + cos(itk::Math::pi*(2 * n / (alpha*(width - 1)) - 1))) / 2; - } - else if (n >= (width - 1)*(1 - alpha / 2)) + if (alphaHighPass > 0.00001) { - imageData[reference->GetDimension(0)*(int)(n + center - (width / 2))] = (1 + cos(itk::Math::pi*(2 * n / (alpha*(width - 1)) + 1 - 2 / alpha))) / 2; + imageData[reference->GetDimension(0)*(int)(n + center - (width / 2))] = + (1 + cos(itk::Math::pi*(2 * n / (alphaHighPass*(width - 1)) - 1))) / 2; } else { imageData[reference->GetDimension(0)*(int)(n + center - (width / 2))] = 1; } } - } - else - { - for (int n = 0; n < width; ++n) + else if (n >= (width - 1)*(1 - alphaLowPass / 2)) //??? { - 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; + if (alphaLowPass > 0.00001) + { + imageData[reference->GetDimension(0)*(int)(n + center - (width / 2))] = + (1 + cos(itk::Math::pi*(2 * n / (alphaLowPass*(width - 1)) + 1 - 2 / alphaLowPass))) / 2; + } + else + { + imageData[reference->GetDimension(0)*(int)(n + center - (width / 2))] = 1; + } } + //MITK_INFO << "n:" << n << " is " << imageData[reference->GetDimension(0)*(int)(n + center - (width / 2))]; } - - // 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)); - } - */ + MITK_INFO << "width: " << width << ", center: " << center << ", alphaHighPass: " << alphaHighPass << ", alphaLowPass: " << alphaLowPass; // mirror the first half of the image for (unsigned int n = reference->GetDimension(1) / 2; n < reference->GetDimension(1); ++n) { imageData[reference->GetDimension(0)*n] = imageData[(reference->GetDimension(1) - (n + 1)) * reference->GetDimension(0)]; } // copy and paste to all lines for (unsigned int line = 1; line < reference->GetDimension(0); ++line) { for (unsigned int sample = 0; sample < reference->GetDimension(1); ++sample) { imageData[reference->GetDimension(0)*sample + line] = imageData[reference->GetDimension(0)*sample]; } } typedef itk::Image< float, 3U > ImageType; ImageType::RegionType region; ImageType::IndexType start; start.Fill(0); region.SetIndex(start); ImageType::SizeType size; size[0] = reference->GetDimension(0); size[1] = reference->GetDimension(1); size[2] = reference->GetDimension(2); region.SetSize(size); ImageType::SpacingType SpacingItk; SpacingItk[0] = reference->GetGeometry()->GetSpacing()[0]; SpacingItk[1] = reference->GetGeometry()->GetSpacing()[1]; SpacingItk[2] = reference->GetGeometry()->GetSpacing()[2]; ImageType::Pointer image = ImageType::New(); image->SetRegions(region); image->Allocate(); image->FillBuffer(itk::NumericTraits::Zero); image->SetSpacing(SpacingItk); ImageType::IndexType pixelIndex; for (unsigned int slice = 0; slice < reference->GetDimension(2); ++slice) { for (unsigned int line = 0; line < reference->GetDimension(0); ++line) { for (unsigned int sample = 0; sample < reference->GetDimension(1); ++sample) { pixelIndex[0] = line; pixelIndex[1] = sample; pixelIndex[2] = slice; image->SetPixel(pixelIndex, imageData[line + sample*reference->GetDimension(0)]); } } } delete[] imageData; return image; } diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/PAImageProcessing.cpp b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/PAImageProcessing.cpp index 2960377da6..36f37eadde 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 @@ -1,1161 +1,1166 @@ /*=================================================================== 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), 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(LowerSliceBoundChanged())); connect(m_Controls.boundHigh, SIGNAL(valueChanged(int)), this, SLOT(UpperSliceBoundChanged())); connect(m_Controls.Partial, SIGNAL(clicked()), this, SLOT(SliceBoundsEnabled())); connect(m_Controls.BatchProcessing, SIGNAL(clicked()), this, SLOT(BatchProcessing())); connect(m_Controls.StepBeamforming, SIGNAL(clicked()), this, SLOT(UpdateSaveBoxes())); connect(m_Controls.StepCropping, SIGNAL(clicked()), this, SLOT(UpdateSaveBoxes())); connect(m_Controls.StepBandpass, SIGNAL(clicked()), this, SLOT(UpdateSaveBoxes())); connect(m_Controls.StepBMode, SIGNAL(clicked()), this, SLOT(UpdateSaveBoxes())); UpdateSaveBoxes(); m_Controls.DoResampling->setChecked(false); m_Controls.ResamplingValue->setEnabled(false); m_Controls.progressBar->setMinimum(0); m_Controls.progressBar->setMaximum(100); m_Controls.progressBar->setVisible(false); m_Controls.UseImageSpacing->setToolTip("Image spacing of y-Axis must be in us, x-Axis in mm."); m_Controls.UseImageSpacing->setToolTipDuration(5000); m_Controls.ProgressInfo->setVisible(false); m_Controls.UseBP->hide(); m_Controls.UseGPUBmode->hide(); #ifndef PHOTOACOUSTICS_USE_GPU m_Controls.UseGPUBf->setEnabled(false); m_Controls.UseGPUBf->setChecked(false); m_Controls.UseGPUBmode->setEnabled(false); m_Controls.UseGPUBmode->setChecked(false); #endif UseImageSpacing(); } void PAImageProcessing::ChangedSOSBandpass() { m_Controls.SpeedOfSound->setValue(m_Controls.BPSpeedOfSound->value()); } void PAImageProcessing::ChangedSOSBeamforming() { m_Controls.BPSpeedOfSound->setValue(m_Controls.SpeedOfSound->value()); } std::vector splitpath( const std::string& str , const std::set delimiters) { std::vector result; char const* pch = str.c_str(); char const* start = pch; for (; *pch; ++pch) { if (delimiters.find(*pch) != delimiters.end()) { if (start != pch) { std::string str(start, pch); result.push_back(str); } else { result.push_back(""); } start = pch + 1; } } result.push_back(start); return result; } void PAImageProcessing::UpdateSaveBoxes() { if (m_Controls.StepBeamforming->isChecked()) m_Controls.SaveBeamforming->setEnabled(true); else m_Controls.SaveBeamforming->setEnabled(false); if (m_Controls.StepCropping->isChecked()) m_Controls.SaveCropping->setEnabled(true); else m_Controls.SaveCropping->setEnabled(false); if (m_Controls.StepBandpass->isChecked()) m_Controls.SaveBandpass->setEnabled(true); else m_Controls.SaveBandpass->setEnabled(false); if (m_Controls.StepBMode->isChecked()) m_Controls.SaveBMode->setEnabled(true); else m_Controls.SaveBMode->setEnabled(false); } void PAImageProcessing::BatchProcessing() { QFileDialog LoadDialog(nullptr, "Select Files to be processed"); LoadDialog.setFileMode(QFileDialog::FileMode::ExistingFiles); LoadDialog.setNameFilter(tr("Images (*.nrrd)")); LoadDialog.setViewMode(QFileDialog::Detail); QStringList fileNames; if (LoadDialog.exec()) fileNames = LoadDialog.selectedFiles(); QString saveDir = QFileDialog::getExistingDirectory(nullptr, tr("Select Directory To Save To"), "", QFileDialog::ShowDirsOnly | QFileDialog::DontResolveSymlinks); DisableControls(); std::set delims{'/'}; bool doSteps[] = { m_Controls.StepBeamforming->isChecked(), m_Controls.StepCropping->isChecked() , m_Controls.StepBandpass->isChecked(), m_Controls.StepBMode->isChecked() }; bool saveSteps[] = { m_Controls.SaveBeamforming->isChecked(), m_Controls.SaveCropping->isChecked() , m_Controls.SaveBandpass->isChecked(), m_Controls.SaveBMode->isChecked() }; for (int fileNumber = 0; fileNumber < fileNames.size(); ++fileNumber) { m_Controls.progressBar->setValue(0); m_Controls.progressBar->setVisible(true); m_Controls.ProgressInfo->setVisible(true); m_Controls.ProgressInfo->setText("loading file"); QString filename = fileNames.at(fileNumber); auto split = splitpath(filename.toStdString(), delims); std::string imageName = split.at(split.size()-1); // remove ".nrrd" imageName = imageName.substr(0, imageName.size()-5); mitk::Image::Pointer image = mitk::IOUtil::Load(filename.toStdString().c_str()); UpdateBFSettings(image); // Beamforming if (doSteps[0]) { std::function progressHandle = [this](int progress, std::string progressInfo) { this->UpdateProgress(progress, progressInfo); }; m_Controls.progressBar->setValue(100); std::string errorMessage = ""; image = m_FilterBank->ApplyBeamforming(image, BFconfig, errorMessage, progressHandle); if (saveSteps[0]) { std::string saveFileName = saveDir.toStdString() + "/" + imageName + " beamformed" + ".nrrd"; mitk::IOUtil::Save(image, saveFileName); } } // Cropping if (doSteps[1]) { m_Controls.ProgressInfo->setText("cropping image"); image = m_FilterBank->ApplyCropping(image, m_Controls.CutoffAbove->value(), m_Controls.CutoffBelow->value(), 0, 0, 0, image->GetDimension(2) - 1); if (saveSteps[1]) { std::string saveFileName = saveDir.toStdString() + "/" + imageName + " cropped" + ".nrrd"; mitk::IOUtil::Save(image, saveFileName); } } // Bandpass if (doSteps[2]) { m_Controls.ProgressInfo->setText("applying bandpass"); float recordTime = image->GetDimension(1)*image->GetGeometry()->GetSpacing()[1] / 1000 / m_Controls.BPSpeedOfSound->value(); // add a safeguard so the program does not chrash when applying a Bandpass that reaches out of the bounds of the image float maxFrequency = 1 / (recordTime / image->GetDimension(1)) * image->GetDimension(1) / 2 / 2 / 1000; float BPHighPass = 1000000 * m_Controls.BPhigh->value(); // [Hz] float BPLowPass = maxFrequency - 1000000 * m_Controls.BPlow->value(); // [Hz] if (BPLowPass > maxFrequency && m_Controls.UseBP->isChecked()) { QMessageBox Msgbox; Msgbox.setText("LowPass too low, disabled it."); Msgbox.exec(); BPLowPass = 0; } if (BPLowPass < 0 && m_Controls.UseBP->isChecked()) { QMessageBox Msgbox; Msgbox.setText("LowPass too high, disabled it."); Msgbox.exec(); BPLowPass = 0; } if (BPHighPass > maxFrequency && m_Controls.UseBP->isChecked()) { QMessageBox Msgbox; Msgbox.setText("HighPass too high, disabled it."); Msgbox.exec(); BPHighPass = 0; } if (BPHighPass > maxFrequency - BFconfig.BPLowPass) { QMessageBox Msgbox; Msgbox.setText("HighPass higher than LowPass, disabled both."); Msgbox.exec(); BPHighPass = 0; BPLowPass = 0; } - image = m_FilterBank->BandpassFilter(image, recordTime, BPHighPass, BPLowPass, m_Controls.BPFalloff->value()); + image = m_FilterBank->BandpassFilter(image, recordTime, BPHighPass, BPLowPass, + m_Controls.BPFalloffHigh->value(), + m_Controls.BPFalloffLow->value()); if (saveSteps[2]) { std::string saveFileName = saveDir.toStdString() + "/" + imageName + " bandpassed" + ".nrrd"; mitk::IOUtil::Save(image, saveFileName); } } // Bmode if (doSteps[3]) { m_Controls.ProgressInfo->setText("applying bmode filter"); bool useGPU = m_Controls.UseGPUBmode->isChecked(); if (m_Controls.BModeMethod->currentText() == "Absolute Filter") image = m_FilterBank->ApplyBmodeFilter(image, mitk::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->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::BeamformingSettings::BeamformingAlgorithm::DAS) newNodeName << "DAS bf, "; else if (BFconfig.Algorithm == mitk::BeamformingSettings::BeamformingAlgorithm::DMAS) newNodeName << "DMAS bf, "; if (BFconfig.DelayCalculationMethod == mitk::BeamformingSettings::DelayCalc::QuadApprox) newNodeName << "q. delay"; 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); levelWindow.SetAuto(image, true, true); newNode->SetLevelWindow(levelWindow); // add new node to data storage this->GetDataStorage()->Add(newNode); // disable progress bar m_Controls.progressBar->setVisible(false); m_Controls.ProgressInfo->setVisible(false); m_Controls.buttonApplyBeamforming->setText("Apply Beamforming"); EnableControls(); // update rendering mitk::RenderingManager::GetInstance()->InitializeViews(image->GetGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void PAImageProcessing::StartBmodeThread() { QList nodes = this->GetDataManagerSelection(); if (nodes.empty()) return; mitk::DataStorage::Pointer storage = this->GetDataStorage(); mitk::DataNode::Pointer node = nodes.front(); if (!node) { // Nothing selected. Inform the user and return QMessageBox::information(NULL, "Template", "Please load and select an image before starting image processing."); return; } mitk::BaseData* data = node->GetData(); if (data) { // test if this data item is an image or not (could also be a surface or something totally different) mitk::Image* image = dynamic_cast(data); if (image) { UpdateBFSettings(image); std::stringstream message; std::string name; message << "Performing image processing for image "; if (node->GetName(name)) { // a property called "name" was found for this DataNode message << "'" << name << "'"; m_OldNodeName = name; } else m_OldNodeName = " "; message << "."; MITK_INFO << message.str(); m_Controls.buttonApplyBModeFilter->setText("working..."); DisableControls(); BmodeThread *thread = new BmodeThread(); connect(thread, &BmodeThread::result, this, &PAImageProcessing::HandleBmodeResults); connect(thread, &BmodeThread::finished, thread, &QObject::deleteLater); bool useGPU = m_Controls.UseGPUBmode->isChecked(); if(m_Controls.BModeMethod->currentText() == "Absolute Filter") thread->setConfig(m_UseLogfilter, m_ResampleSpacing, mitk::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(), 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->setConfig(BPHighPass, BPLowPass, m_Controls.BPFalloffLow->value(), m_Controls.BPFalloffHigh->value(), recordTime); thread->setInputImage(image); thread->setFilterBank(m_FilterBank); MITK_INFO << "Started new thread for Bandpass filter"; thread->start(); } } } void PAImageProcessing::HandleBandpassResults(mitk::Image::Pointer image) { auto newNode = mitk::DataNode::New(); newNode->SetData(image); // name the new Data node std::stringstream newNodeName; newNodeName << m_OldNodeName << " "; newNodeName << "Bandpassed"; newNode->SetName(newNodeName.str()); // update level window for the current dynamic range mitk::LevelWindow levelWindow; newNode->GetLevelWindow(levelWindow); auto data = newNode->GetData(); levelWindow.SetAuto(dynamic_cast(data), true, true); newNode->SetLevelWindow(levelWindow); // add new node to data storage this->GetDataStorage()->Add(newNode); m_Controls.buttonApplyBandpass->setText("Apply Bandpass"); EnableControls(); // update rendering mitk::RenderingManager::GetInstance()->InitializeViews( dynamic_cast(data)->GetGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void PAImageProcessing::SliceBoundsEnabled() { if (!m_Controls.Partial->isChecked()) { m_Controls.boundLow->setEnabled(false); m_Controls.boundHigh->setEnabled(false); return; } else { m_Controls.boundLow->setEnabled(true); m_Controls.boundHigh->setEnabled(true); } } void PAImageProcessing::UpperSliceBoundChanged() { if(m_Controls.boundLow->value() > m_Controls.boundHigh->value()) { m_Controls.boundLow->setValue(m_Controls.boundHigh->value()); } } void PAImageProcessing::LowerSliceBoundChanged() { if (m_Controls.boundLow->value() > m_Controls.boundHigh->value()) { m_Controls.boundHigh->setValue(m_Controls.boundLow->value()); } } void PAImageProcessing::UpdateProgress(int progress, std::string progressInfo) { if (progress < 100) m_Controls.progressBar->setValue(progress); else m_Controls.progressBar->setValue(100); m_Controls.ProgressInfo->setText(progressInfo.c_str()); qApp->processEvents(); } void PAImageProcessing::PAMessageBox(std::string message) { if (0 != message.compare("noMessage")) { QMessageBox msgBox; msgBox.setText(message.c_str()); msgBox.exec(); } } void PAImageProcessing::UpdateImageInfo() { QList nodes = this->GetDataManagerSelection(); if (nodes.empty()) return; mitk::DataNode::Pointer node = nodes.front(); if (!node) { // Nothing selected return; } mitk::BaseData* data = node->GetData(); if (data) { // test if this data item is an image or not (could also be a surface or something totally different) mitk::Image* image = dynamic_cast(data); if (image) { // beamforming configs if (m_Controls.UseImageSpacing->isChecked()) { m_Controls.ElementCount->setValue(image->GetDimension(0)); m_Controls.Pitch->setValue(image->GetGeometry()->GetSpacing()[0]); } m_Controls.boundLow->setMaximum(image->GetDimension(2) - 1); m_Controls.boundHigh->setMaximum(image->GetDimension(2) - 1); UpdateBFSettings(image); m_Controls.CutoffBeforeBF->setValue(0.000001 / BFconfig.TimeSpacing); // 1us standard offset for our transducer std::stringstream frequency; 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::BeamformingSettings::BeamformingAlgorithm::DAS; else if ("DMAS" == m_Controls.BFAlgorithm->currentText()) 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::BeamformingSettings::DelayCalc::QuadApprox; } else if ("Spherical Wave" == m_Controls.DelayCalculation->currentText()) { BFconfig.DelayCalculationMethod = mitk::BeamformingSettings::DelayCalc::Spherical; } if ("Von Hann" == m_Controls.Apodization->currentText()) { BFconfig.Apod = mitk::BeamformingSettings::Apodization::Hann; } else if ("Hamming" == m_Controls.Apodization->currentText()) { BFconfig.Apod = mitk::BeamformingSettings::Apodization::Hamm; } else if ("Box" == m_Controls.Apodization->currentText()) { 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.UseGPUBf->isChecked(); BFconfig.upperCutoff = m_Controls.CutoffBeforeBF->value(); 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 / 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.isPhotoacousticImage = false; } else if ("PA Image" == m_Controls.ImageType->currentText()) { 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.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); #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.BPFalloffLow->setEnabled(true); + m_Controls.BPFalloffHigh->setEnabled(true); m_Controls.UseImageSpacing->setEnabled(true); UseImageSpacing(); m_Controls.Pitch->setEnabled(true); m_Controls.ElementCount->setEnabled(true); m_Controls.SpeedOfSound->setEnabled(true); m_Controls.Samples->setEnabled(true); m_Controls.Lines->setEnabled(true); m_Controls.Angle->setEnabled(true); m_Controls.buttonApplyBeamforming->setEnabled(true); } void PAImageProcessing::DisableControls() { m_Controls.BatchProcessing->setEnabled(false); m_Controls.StepBeamforming->setEnabled(false); m_Controls.StepBandpass->setEnabled(false); m_Controls.StepCropping->setEnabled(false); m_Controls.StepBMode->setEnabled(false); m_Controls.SaveBeamforming->setEnabled(false); m_Controls.SaveBandpass->setEnabled(false); m_Controls.SaveCropping->setEnabled(false); m_Controls.SaveBMode->setEnabled(false); m_Controls.DoResampling->setEnabled(false); m_Controls.ResamplingValue->setEnabled(false); m_Controls.Logfilter->setEnabled(false); m_Controls.BModeMethod->setEnabled(false); m_Controls.buttonApplyBModeFilter->setEnabled(false); m_Controls.CutoffAbove->setEnabled(false); m_Controls.CutoffBelow->setEnabled(false); m_Controls.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); #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.BPFalloffLow->setEnabled(false); + m_Controls.BPFalloffHigh->setEnabled(false); m_Controls.UseImageSpacing->setEnabled(false); m_Controls.ScanDepth->setEnabled(false); m_Controls.Pitch->setEnabled(false); m_Controls.ElementCount->setEnabled(false); m_Controls.SpeedOfSound->setEnabled(false); m_Controls.Samples->setEnabled(false); m_Controls.Lines->setEnabled(false); m_Controls.Angle->setEnabled(false); m_Controls.buttonApplyBeamforming->setEnabled(false); } void PAImageProcessing::UseImageSpacing() { if (m_Controls.UseImageSpacing->isChecked()) { m_Controls.ScanDepth->setDisabled(true); } else { m_Controls.ScanDepth->setEnabled(true); } } #include void BeamformingThread::run() { mitk::Image::Pointer resultImage = mitk::Image::New(); mitk::Image::Pointer resultImageBuffer; std::string errorMessage = ""; std::function progressHandle = [this](int progress, std::string progressInfo) { emit updateProgress(progress, progressInfo); }; resultImageBuffer = m_FilterBank->ApplyBeamforming(m_InputImage, m_BFconfig, errorMessage, progressHandle); mitk::ImageReadAccessor copy(resultImageBuffer); resultImage->Initialize(resultImageBuffer); resultImage->SetSpacing(resultImageBuffer->GetGeometry()->GetSpacing()); resultImage->SetImportVolume(const_cast(copy.GetData()), 0, 0, mitk::Image::CopyMemory); emit result(resultImage); emit message(errorMessage); } void BeamformingThread::setConfig(mitk::BeamformingSettings BFconfig) { m_BFconfig = BFconfig; } void BeamformingThread::setInputImage(mitk::Image::Pointer image) { m_InputImage = image; } void BmodeThread::run() { mitk::Image::Pointer resultImage; resultImage = m_FilterBank->ApplyBmodeFilter(m_InputImage, m_Method, m_UseGPU, m_UseLogfilter, m_ResampleSpacing); emit result(resultImage); } void BmodeThread::setConfig(bool useLogfilter, double resampleSpacing, mitk::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; resultImage = m_FilterBank->ApplyCropping(m_InputImage, m_CutAbove, m_CutBelow, 0, 0, m_CutSliceFirst, m_CutSliceLast); emit result(resultImage); } void CropThread::setConfig(unsigned int CutAbove, unsigned int CutBelow, unsigned int CutSliceFirst, unsigned int CutSliceLast) { m_CutAbove = CutAbove; m_CutBelow = CutBelow; m_CutSliceLast = CutSliceLast; m_CutSliceFirst = CutSliceFirst; } void CropThread::setInputImage(mitk::Image::Pointer image) { m_InputImage = image; } void BandpassThread::run() { mitk::Image::Pointer resultImage; - resultImage = m_FilterBank->BandpassFilter(m_InputImage, m_RecordTime, m_BPHighPass, m_BPLowPass, m_TukeyAlpha); + resultImage = m_FilterBank->BandpassFilter(m_InputImage, m_RecordTime, m_BPHighPass, m_BPLowPass, m_TukeyAlphaHighPass, m_TukeyAlphaLowPass); emit result(resultImage); } -void BandpassThread::setConfig(float BPHighPass, float BPLowPass, float TukeyAlpha, float recordTime) +void BandpassThread::setConfig(float BPHighPass, float BPLowPass, float TukeyAlphaHighPass, float TukeyAlphaLowPass, float recordTime) { m_BPHighPass = BPHighPass; m_BPLowPass = BPLowPass; - m_TukeyAlpha = TukeyAlpha; + m_TukeyAlphaHighPass = TukeyAlphaHighPass; + m_TukeyAlphaLowPass = TukeyAlphaLowPass; m_RecordTime = recordTime; } void BandpassThread::setInputImage(mitk::Image::Pointer image) { m_InputImage = image; } diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/PAImageProcessing.h b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/PAImageProcessing.h index d20b78b3ae..8bb5eb860e 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 @@ -1,254 +1,255 @@ /*=================================================================== 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: void UpperSliceBoundChanged(); void LowerSliceBoundChanged(); void SliceBoundsEnabled(); void UseResampling(); void UseLogfilter(); void SetResampling(); void UseImageSpacing(); void UpdateImageInfo(); /** \brief Method called when the beamforming thread finishes; * it adds the image to a new data node and registers it to the worbench's data storage */ void HandleBeamformingResults(mitk::Image::Pointer image); /** \brief Beamforming is being performed in a separate thread to keep the workbench from freezing. */ void StartBeamformingThread(); /** \brief Method called when the B-mode filter thread finishes; * it adds the image to a new data node and registers it to the worbench's data storage */ void HandleBmodeResults(mitk::Image::Pointer image); /** \brief B-mode filtering is being performed in a separate thread to keep the workbench from freezing. */ void StartBmodeThread(); /** \brief Method called when the Cropping thread finishes; * it adds the image to a new data node and registers it to the worbench's data storage */ void HandleCropResults(mitk::Image::Pointer image); /** \brief Cropping is being performed in a separate thread to keep the workbench from freezing. */ void StartCropThread(); /** \brief Method called when the bandpass thread finishes; * it adds the image to a new data node and registers it to the worbench's data storage */ void HandleBandpassResults(mitk::Image::Pointer image); /** \brief Bandpassing is being performed in a separate thread to keep the workbench from freezing. */ void StartBandpassThread(); void UpdateProgress(int progress, std::string progressInfo); void PAMessageBox(std::string message); void BatchProcessing(); void UpdateSaveBoxes(); void ChangedSOSBandpass(); void ChangedSOSBeamforming(); protected: virtual void CreateQtPartControl(QWidget *parent) override; virtual void SetFocus() override; /** \brief called by QmitkFunctionality when DataManager's selection has changed. * On a change some parameters are internally updated to calculate bounds for GUI elements as the slice selector for beamforming or * the bandpass filter settings. */ virtual void OnSelectionChanged( berry::IWorkbenchPart::Pointer source, const QList& nodes ) override; /** \brief Instance of the GUI controls */ Ui::PAImageProcessingControls m_Controls; float m_ResampleSpacing; bool m_UseLogfilter; std::string m_OldNodeName; /** \brief The settings set which is used for beamforming, updated through this class. */ mitk::BeamformingSettings 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::BeamformingSettings BFconfig); void setInputImage(mitk::Image::Pointer image); void setFilterBank(mitk::PhotoacousticImage::Pointer filterBank) { m_FilterBank = filterBank; } protected: 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, 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, 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 setConfig(float BPHighPass, float BPLowPass, float TukeyAlphaHighPass, float TukeyAlphaLowPass, 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_TukeyAlphaHighPass; + float m_TukeyAlphaLowPass; 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 fcd6e415c8..2cf6316fd3 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 @@ -1,991 +1,1027 @@ PAImageProcessingControls 0 0 - 382 + 385 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 + false Save - true + false Save + + true + 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 + Envelope Detection Absolute Filter Envelope Detection Do Resampling true 0 0 13 0 11 3 0.010000000000000 1.000000000000000 0.010000000000000 - 0.075000000000000 + 0.150000000000000 [mm] Resampled Depth Spacing - Add Logfilter + Logarithmic Compression 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 + 1.000000000000000 [MHz] f High Pass [MHz] f Low Pass 0 0 3 200.000000000000000 - - - - Tukey window alpha - - - - + 1 200.000000000000000 3000.000000000000000 5.000000000000000 1540.000000000000000 - + [m/s] Speed of Sound - - + + + + 1.000000000000000 + + + 0.100000000000000 + + + 0.500000000000000 + + + + + + + Tukey Window α High Pass + + + + + 2 1.000000000000000 0.100000000000000 - 0.500000000000000 + 0.000000000000000 + + + + + + + Tukey Window α Low Pass <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 - 10 + 300 Cut Top Cut Bottom 99999 5 - 165 + 800 <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 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 0 0 DAS DMAS sDMAS 0 0 - Quad. Approx. + Spherical Wave 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 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> + + + + Qt::Vertical + + + + 20 + 40 + + + +