diff --git a/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticFilterService.h b/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticFilterService.h index db7df823bc..23c13bca1d 100644 --- a/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticFilterService.h +++ b/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticFilterService.h @@ -1,128 +1,128 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef mitkPhotoacousticFilterService_H_HEADER_INCLUDED #define mitkPhotoacousticFilterService_H_HEADER_INCLUDED #include "itkObject.h" #include "mitkCommon.h" #include "mitkImage.h" #include #include "mitkBeamformingSettings.h" #include "mitkBeamformingFilter.h" #include "MitkPhotoacousticsAlgorithmsExports.h" namespace mitk { /*! * \brief Class holding methods to apply all Filters within the Photoacoustics Algorithms Module * * Implemented are: * - A B-Mode Filter * - A Resampling Filter * - Beamforming on GPU and CPU * - A Bandpass Filter */ class MITKPHOTOACOUSTICSALGORITHMS_EXPORT PhotoacousticFilterService : public itk::Object { public: mitkClassMacroItkParent(mitk::PhotoacousticFilterService, itk::Object); itkFactorylessNewMacro(Self); /** \brief Defines the methods for the B-Mode filter * Currently implemented are an Envelope Detection filter and a simple Absolute filter. */ enum BModeMethod { EnvelopeDetection, Abs }; /** \brief Applies a B-Mode Filter * * Applies a B-Mode filter using the given parameters. * @param inputImage The image to be processed. * @param method The kind of B-Mode Filter to be used. * @param 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 UseLogFilter = false); /** \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, double* outputSpacing); mitk::Image::Pointer ApplyResamplingToDim(mitk::Image::Pointer inputImage, double* outputDimension); /** \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 progressHandle An std::function, through which progress of the currently updating filter is reported. * The integer argument is a number between 0 an 100 to indicate how far completion has been achieved, the std::string argument indicates what the filter is currently doing. * @return The processed image is returned after the filter has finished. */ mitk::Image::Pointer ApplyBeamforming(mitk::Image::Pointer inputImage, BeamformingSettings::Pointer config, std::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); + mitk::Image::Pointer ApplyCropping(mitk::Image::Pointer inputImage, int above, int below, int right, int left, int minSlice, int maxSlice, int* errCode); /** \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 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 alphaHighPass The high pass tukey window parameter to control the shape of the bandpass filter: 0 will make it a Box function, 1 a Hann function. alpha can be set between those two bounds. * @param alphaLowPass The low passtukey window parameter to control the shape of the bandpass filter: 0 will make it a Box function, 1 a Hann function. alpha can be set between those two bounds. * @return The processed image is returned after the filter has finished. */ mitk::Image::Pointer ApplyBandpassFilter(mitk::Image::Pointer data, float BPHighPass, float BPLowPass, float alphaHighPass, float alphaLowPass, float timeSpacing, float SpeedOfSound, bool IsBFImage); protected: PhotoacousticFilterService(); ~PhotoacousticFilterService() override; /** \brief For performance reasons, an instance of the Beamforming filter is initialized as soon as possible and kept for all further uses. */ mitk::BeamformingFilter::Pointer m_BeamformingFilter; mitk::Image::Pointer ConvertToFloat(mitk::Image::Pointer); }; } // namespace mitk #endif /* mitkPhotoacousticFilterService_H_HEADER_INCLUDED */ diff --git a/Modules/PhotoacousticsAlgorithms/source/filters/mitkCropImageFilter.cpp b/Modules/PhotoacousticsAlgorithms/source/filters/mitkCropImageFilter.cpp index 3996284f79..b8b74bb417 100644 --- a/Modules/PhotoacousticsAlgorithms/source/filters/mitkCropImageFilter.cpp +++ b/Modules/PhotoacousticsAlgorithms/source/filters/mitkCropImageFilter.cpp @@ -1,120 +1,120 @@ /*=================================================================== mitkCropImageFilter The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkCropImageFilter.h" #include #include mitk::CropImageFilter::CropImageFilter() : m_XPixelsCropStart(0), m_YPixelsCropStart(0), m_ZPixelsCropStart(0), m_XPixelsCropEnd(0), m_YPixelsCropEnd(0), m_ZPixelsCropEnd(0) { MITK_INFO << "Instantiating CropImageFilter..."; SetNumberOfIndexedInputs(1); SetNumberOfIndexedOutputs(1); MITK_INFO << "Instantiating CropImageFilter...[Done]"; } mitk::CropImageFilter::~CropImageFilter() { MITK_INFO << "Destructed CastToFloatImageFilter."; } void mitk::CropImageFilter::SanityCheckPreconditions() { mitk::Image::Pointer inputImage = GetInput(); std::string type = inputImage->GetPixelType().GetTypeAsString(); if (!(type == "scalar (float)" || type == " (float)")) { MITK_ERROR << "This filter can currently only handle float type images."; mitkThrow() << "This filter can currently only handle float type images."; } if (m_XPixelsCropStart + m_XPixelsCropEnd >= inputImage->GetDimension(0)) { MITK_ERROR << "X Crop area too large for selected input image"; mitkThrow() << "X Crop area too large for selected input image"; } if (m_YPixelsCropStart + m_YPixelsCropEnd >= inputImage->GetDimension(1)) { MITK_ERROR << "Y Crop area too large for selected input image"; mitkThrow() << "Y Crop area too large for selected input image"; } if (inputImage->GetDimension() == 3) { if (m_ZPixelsCropStart + m_ZPixelsCropEnd >= inputImage->GetDimension(2)) { MITK_INFO << m_ZPixelsCropStart + m_ZPixelsCropEnd << "vs" << inputImage->GetDimension(2); MITK_ERROR << "Z Crop area too large for selected input image"; mitkThrow() << "Z Crop area too large for selected input image"; } } else { if (m_ZPixelsCropStart + m_ZPixelsCropEnd > 0) { mitkThrow() << "Z Crop area too large for selected input image"; } } } void mitk::CropImageFilter::GenerateData() { mitk::Image::Pointer inputImage = GetInput(); mitk::Image::Pointer outputImage = GetOutput(); SanityCheckPreconditions(); unsigned int* outputDim; unsigned int* inputDim = inputImage->GetDimensions(); if (inputImage->GetDimension() == 2) outputDim = new unsigned int[2]{ inputImage->GetDimension(0) - m_XPixelsCropStart - m_XPixelsCropEnd, inputImage->GetDimension(1) - m_YPixelsCropStart - m_YPixelsCropEnd }; else outputDim = new unsigned int[3]{ inputImage->GetDimension(0) - m_XPixelsCropStart - m_XPixelsCropEnd, inputImage->GetDimension(1) - m_YPixelsCropStart - m_YPixelsCropEnd, inputImage->GetDimension(2) - m_ZPixelsCropStart - m_ZPixelsCropEnd }; outputImage->Initialize(mitk::MakeScalarPixelType(), inputImage->GetDimension(), outputDim); outputImage->SetSpacing(inputImage->GetGeometry()->GetSpacing()); ImageReadAccessor accR(inputImage); const float* inputData = (const float*)(accR.GetData()); ImageWriteAccessor accW(outputImage); float* outputData = (float*)(accW.GetData()); - unsigned int zLength = inputImage->GetDimension() == 3 ? outputDim[2] : 0; + unsigned int zLength = inputImage->GetDimension() == 3 ? outputDim[2] : 1; for (unsigned int sl = 0; sl < zLength; ++sl) { for (unsigned int l = 0; l < outputDim[0]; ++l) { for (unsigned int s = 0; s < outputDim[1]; ++s) { outputData[l + s*outputDim[0] + sl*outputDim[0] * outputDim[1]] = inputData[(l + m_XPixelsCropStart) + (s + m_YPixelsCropStart)*inputDim[0] + (sl + m_ZPixelsCropStart)*inputDim[0] * inputDim[1]]; } } } delete[] outputDim; } diff --git a/Modules/PhotoacousticsAlgorithms/source/utils/mitkPhotoacousticFilterService.cpp b/Modules/PhotoacousticsAlgorithms/source/utils/mitkPhotoacousticFilterService.cpp index 767faed27a..9524e1db36 100644 --- a/Modules/PhotoacousticsAlgorithms/source/utils/mitkPhotoacousticFilterService.cpp +++ b/Modules/PhotoacousticsAlgorithms/source/utils/mitkPhotoacousticFilterService.cpp @@ -1,276 +1,282 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkPhotoacousticFilterService.h" #include "mitkITKImageImport.h" #include #include #include "./OpenCLFilter/mitkPhotoacousticBModeFilter.h" #include "mitkConvert2Dto3DImageFilter.h" #include #include "../ITKFilter/ITKUltrasound/itkBModeImageFilter.h" #include "../ITKFilter/itkPhotoacousticBModeImageFilter.h" #include // itk dependencies #include "itkImage.h" #include "itkResampleImageFilter.h" #include "itkCastImageFilter.h" #include "itkCropImageFilter.h" #include "itkRescaleIntensityImageFilter.h" #include "itkIntensityWindowingImageFilter.h" #include #include "itkBSplineInterpolateImageFunction.h" #include // needed itk image filters #include "mitkImageCast.h" mitk::PhotoacousticFilterService::PhotoacousticFilterService() { MITK_INFO << "[PhotoacousticFilterService] created filter service"; } mitk::PhotoacousticFilterService::~PhotoacousticFilterService() { MITK_INFO << "[PhotoacousticFilterService] destructed filter service"; } mitk::Image::Pointer mitk::PhotoacousticFilterService::ApplyBmodeFilter( mitk::Image::Pointer inputImage, BModeMethod method, bool UseLogFilter) { // 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; auto floatImage = ConvertToFloat(inputImage); if (method == BModeMethod::Abs) { PhotoacousticBModeFilter::Pointer filter = PhotoacousticBModeFilter::New(); filter->UseLogFilter(UseLogFilter); filter->SetInput(floatImage); filter->Update(); return filter->GetOutput(); } 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(floatImage, itkImage); if (UseLogFilter) { bModeFilter->SetInput(itkImage); bModeFilter->SetDirection(1); itkImage = bModeFilter->GetOutput(); } else { photoacousticBModeFilter->SetInput(itkImage); photoacousticBModeFilter->SetDirection(1); itkImage = photoacousticBModeFilter->GetOutput(); } return mitk::GrabItkImageMemory(itkImage); } mitk::Image::Pointer mitk::PhotoacousticFilterService::ApplyResampling( mitk::Image::Pointer inputImage, double *outputSpacing) { typedef itk::Image< float, 3 > itkFloatImageType; auto floatImage = ConvertToFloat(inputImage); typedef itk::ResampleImageFilter < itkFloatImageType, itkFloatImageType > ResampleImageFilter; ResampleImageFilter::Pointer resampleImageFilter = ResampleImageFilter::New(); itkFloatImageType::Pointer itkImage; mitk::CastToItkImage(floatImage, itkImage); itkFloatImageType::SpacingType outputSpacingItk; itkFloatImageType::SizeType inputSizeItk = itkImage->GetLargestPossibleRegion().GetSize(); itkFloatImageType::SizeType outputSizeItk = inputSizeItk; outputSpacingItk[0] = outputSpacing[0]; outputSpacingItk[1] = outputSpacing[1]; outputSpacingItk[2] = itkImage->GetSpacing()[2]; outputSizeItk[0] = outputSizeItk[0] * (floatImage->GetGeometry()->GetSpacing()[0] / outputSpacing[0]); outputSizeItk[1] = outputSizeItk[1] * (floatImage->GetGeometry()->GetSpacing()[1] / outputSpacing[1]); resampleImageFilter->SetInput(itkImage); resampleImageFilter->SetSize(outputSizeItk); resampleImageFilter->SetOutputSpacing(outputSpacingItk); resampleImageFilter->UpdateLargestPossibleRegion(); return mitk::GrabItkImageMemory(resampleImageFilter->GetOutput()); } mitk::Image::Pointer mitk::PhotoacousticFilterService::ApplyResamplingToDim( mitk::Image::Pointer inputImage, double *outputDimension) { typedef itk::Image< float, 3 > itkFloatImageType; auto floatImage = ConvertToFloat(inputImage); typedef itk::ResampleImageFilter < itkFloatImageType, itkFloatImageType > ResampleImageFilter; ResampleImageFilter::Pointer resampleImageFilter = ResampleImageFilter::New(); itkFloatImageType::Pointer itkImage; mitk::CastToItkImage(floatImage, itkImage); itkFloatImageType::SpacingType outputSpacingItk; itkFloatImageType::SizeType inputSizeItk = itkImage->GetLargestPossibleRegion().GetSize(); itkFloatImageType::SizeType outputSizeItk = inputSizeItk; outputSizeItk[0] = outputDimension[0]; outputSizeItk[1] = outputDimension[1]; MITK_INFO << outputSizeItk[0] << " " << outputSizeItk[1]; outputSpacingItk[0] = (double)inputSizeItk[0] / (double)outputSizeItk[0] * floatImage->GetGeometry()->GetSpacing()[0]; outputSpacingItk[1] = (double)inputSizeItk[1] / (double)outputSizeItk[1] * floatImage->GetGeometry()->GetSpacing()[1]; outputSpacingItk[2] = itkImage->GetSpacing()[2]; MITK_INFO << outputSpacingItk[0] << " " << outputSpacingItk[1]; resampleImageFilter->SetInput(itkImage); resampleImageFilter->SetSize(outputSizeItk); resampleImageFilter->SetOutputSpacing(outputSpacingItk); resampleImageFilter->UpdateLargestPossibleRegion(); return mitk::GrabItkImageMemory(resampleImageFilter->GetOutput()); } mitk::Image::Pointer mitk::PhotoacousticFilterService::ApplyCropping( mitk::Image::Pointer inputImage, int above, int below, int right, int left, - int zStart, int zEnd) + int zStart, int zEnd, + int* errCode) { + *errCode = 0; try { auto floatImage = ConvertToFloat(inputImage); mitk::CropImageFilter::Pointer cropImageFilter = mitk::CropImageFilter::New(); cropImageFilter->SetInput(floatImage); cropImageFilter->SetXPixelsCropStart(left); cropImageFilter->SetXPixelsCropEnd(right); cropImageFilter->SetYPixelsCropStart(above); cropImageFilter->SetYPixelsCropEnd(below); cropImageFilter->SetZPixelsCropStart(zStart); cropImageFilter->SetZPixelsCropEnd(zEnd); cropImageFilter->Update(); return cropImageFilter->GetOutput(); } catch (mitk::Exception &e) { std::string errorMessage = "Caught unexpected exception "; errorMessage.append(e.what()); MITK_ERROR << errorMessage; + *errCode = -1; + mitk::Image::Pointer ret = mitk::Image::New(); + unsigned int dim[3] = { 1,1,1 }; + ret->Initialize(MakeScalarPixelType(), 3, dim); - return inputImage; + return ret; } } mitk::Image::Pointer mitk::PhotoacousticFilterService::ApplyBeamforming( mitk::Image::Pointer inputImage, BeamformingSettings::Pointer config, std::function progressHandle) { Image::Pointer processedImage = mitk::Image::New(); if (inputImage->GetDimension() != 3) { mitk::Convert2Dto3DImageFilter::Pointer dimensionImageFilter = mitk::Convert2Dto3DImageFilter::New(); dimensionImageFilter->SetInput(inputImage); dimensionImageFilter->Update(); processedImage = dimensionImageFilter->GetOutput(); } else { processedImage = inputImage; } m_BeamformingFilter = mitk::BeamformingFilter::New(config); m_BeamformingFilter->SetInput(ConvertToFloat(processedImage)); m_BeamformingFilter->SetProgressHandle(progressHandle); m_BeamformingFilter->UpdateLargestPossibleRegion(); processedImage = m_BeamformingFilter->GetOutput(); return processedImage; } mitk::Image::Pointer mitk::PhotoacousticFilterService::ApplyBandpassFilter( mitk::Image::Pointer data, float BPHighPass, float BPLowPass, float alphaHighPass, float alphaLowPass, float TimeSpacing, float SpeedOfSound, bool IsBFImage) { try { auto floatData = ConvertToFloat(data); mitk::BandpassFilter::Pointer bandpassFilter = mitk::BandpassFilter::New(); bandpassFilter->SetInput(floatData); bandpassFilter->SetHighPass(BPHighPass); bandpassFilter->SetLowPass(BPLowPass); bandpassFilter->SetHighPassAlpha(alphaHighPass); bandpassFilter->SetLowPassAlpha(alphaLowPass); bandpassFilter->SetSpeedOfSound(SpeedOfSound); bandpassFilter->SetTimeSpacing(TimeSpacing); bandpassFilter->SetIsBFImage(IsBFImage); bandpassFilter->Update(); return bandpassFilter->GetOutput(); } catch (mitk::Exception &e) { std::string errorMessage = "Caught unexpected exception "; errorMessage.append(e.what()); MITK_ERROR << errorMessage; return data; } } mitk::Image::Pointer mitk::PhotoacousticFilterService::ConvertToFloat(mitk::Image::Pointer inputImage) { if ((inputImage->GetPixelType().GetTypeAsString() == "scalar (float)" || inputImage->GetPixelType().GetTypeAsString() == " (float)")) { return inputImage; } mitk::CastToFloatImageFilter::Pointer castToFloatImageFilter = mitk::CastToFloatImageFilter::New(); castToFloatImageFilter->SetInput(inputImage); castToFloatImageFilter->Update(); return castToFloatImageFilter->GetOutput(); } 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 9cb70d1abc..8f06f32eff 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 @@ -1,1060 +1,1110 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ // Blueberry #include #include // Qmitk #include "PAImageProcessing.h" // Qt #include #include #include #include //mitk image #include #include "mitkPhotoacousticFilterService.h" #include "mitkCastToFloatImageFilter.h" #include "mitkBeamformingFilter.h" //other #include #include #include const std::string PAImageProcessing::VIEW_ID = "org.mitk.views.paimageprocessing"; PAImageProcessing::PAImageProcessing() : m_ResampleSpacing(0), m_UseLogfilter(false), m_FilterBank(mitk::PhotoacousticFilterService::New()) { qRegisterMetaType(); qRegisterMetaType(); } void PAImageProcessing::SetFocus() { m_Controls.buttonApplyBModeFilter->setFocus(); } void PAImageProcessing::CreateQtPartControl(QWidget *parent) { // 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())); connect(m_Controls.UseSignalDelay, SIGNAL(clicked()), this, SLOT(UseSignalDelay())); connect(m_Controls.IsBFImage, SIGNAL(clicked()), this, SLOT(UpdateImageInfo())); UpdateSaveBoxes(); UseSignalDelay(); 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.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::UseSignalDelay() { if (m_Controls.UseSignalDelay->isChecked()) { m_Controls.SignalDelay->setEnabled(true); } else { m_Controls.SignalDelay->setEnabled(false); } } 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()); auto BFconfig = CreateBeamformingSettings(image); // Beamforming if (doSteps[0]) { + if (m_Controls.UseSignalDelay->isChecked()) + { + float signalDelay = m_Controls.SignalDelay->value(); + if (signalDelay != 0) + { + int cropPixels = std::round(signalDelay / BFconfig->GetTimeSpacing() / 1000000); + MITK_INFO << cropPixels; + int errCode = 0; + image = m_FilterBank->ApplyCropping(image, cropPixels, 0, 0, 0, 0, image->GetDimension(2) - 1, &errCode); + + BFconfig = mitk::BeamformingSettings::New(BFconfig->GetPitchInMeters(), BFconfig->GetSpeedOfSound(), + BFconfig->GetTimeSpacing(), BFconfig->GetAngle(), BFconfig->GetIsPhotoacousticImage(), BFconfig->GetSamplesPerLine(), + BFconfig->GetReconstructionLines(), image->GetDimensions(), BFconfig->GetReconstructionDepth(), + BFconfig->GetUseGPU(), BFconfig->GetGPUBatchSize(), BFconfig->GetDelayCalculationMethod(), BFconfig->GetApod(), + BFconfig->GetApodizationArraySize(), BFconfig->GetAlgorithm()); + } + } + std::function progressHandle = [this](int progress, std::string progressInfo) { this->UpdateProgress(progress, progressInfo); }; m_Controls.progressBar->setValue(100); image = m_FilterBank->ApplyBeamforming(image, BFconfig, 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, 0); + int errCode = 0; + image = m_FilterBank->ApplyCropping(image, m_Controls.CutoffAbove->value(), m_Controls.CutoffBelow->value(), 0, 0, 0, 0, &errCode); + + if (errCode == -1) + { + QMessageBox Msgbox; + Msgbox.setText("It has been attempted to cut off more pixels than the image contains. Aborting batch processing."); + Msgbox.exec(); + m_Controls.progressBar->setVisible(false); + EnableControls(); + return; + } 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) { QMessageBox Msgbox; Msgbox.setText("LowPass too low, disabled it."); Msgbox.exec(); BPLowPass = 0; } if (BPLowPass < 0) { QMessageBox Msgbox; Msgbox.setText("LowPass too high, disabled it."); Msgbox.exec(); BPLowPass = 0; } if (BPHighPass > maxFrequency) { QMessageBox Msgbox; Msgbox.setText("HighPass too high, disabled it."); Msgbox.exec(); BPHighPass = 0; } if (BPHighPass > maxFrequency - BPLowPass) { QMessageBox Msgbox; Msgbox.setText("HighPass higher than LowPass, disabled both."); Msgbox.exec(); BPHighPass = 0; BPLowPass = 0; } image = m_FilterBank->ApplyBandpassFilter(image, BPHighPass, BPLowPass, m_Controls.BPFalloffHigh->value(), m_Controls.BPFalloffLow->value(), BFconfig->GetTimeSpacing(), BFconfig->GetSpeedOfSound(), m_Controls.IsBFImage->isChecked()); if (saveSteps[2]) { std::string saveFileName = saveDir.toStdString() + "/" + imageName + " bandpassed" + ".nrrd"; mitk::IOUtil::Save(image, saveFileName); } } // Bmode if (doSteps[3]) { m_Controls.ProgressInfo->setText("applying bmode filter"); if (m_Controls.BModeMethod->currentText() == "Absolute Filter") image = m_FilterBank->ApplyBmodeFilter(image, mitk::PhotoacousticFilterService::BModeMethod::Abs, m_UseLogfilter); else if (m_Controls.BModeMethod->currentText() == "Envelope Detection") image = m_FilterBank->ApplyBmodeFilter(image, mitk::PhotoacousticFilterService::BModeMethod::EnvelopeDetection, m_UseLogfilter); if (m_ResampleSpacing != 0) { double desiredSpacing[2]{ image->GetGeometry()->GetSpacing()[0], m_ResampleSpacing }; image = m_FilterBank->ApplyResampling(image, desiredSpacing); } 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) { auto BFconfig = CreateBeamformingSettings(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"); DisableControls(); BeamformingThread *thread = new BeamformingThread(); connect(thread, &BeamformingThread::result, this, &PAImageProcessing::HandleResults); connect(thread, &BeamformingThread::updateProgress, this, &PAImageProcessing::UpdateProgress); connect(thread, &BeamformingThread::finished, thread, &QObject::deleteLater); thread->setConfig(BFconfig); if (m_Controls.UseSignalDelay->isChecked()) thread->setSignalDelay(m_Controls.SignalDelay->value()); thread->setInputImage(image); thread->setFilterBank(m_FilterBank); MITK_INFO << "Started new thread for Beamforming"; thread->start(); } } } void PAImageProcessing::HandleResults(mitk::Image::Pointer image, std::string nameExtension) { + if (image == nullptr) + { + QMessageBox Msgbox; + Msgbox.setText("An error has occurred during processing; please see the console output."); + Msgbox.exec(); + + // disable progress bar + m_Controls.progressBar->setVisible(false); + m_Controls.ProgressInfo->setVisible(false); + EnableControls(); + + return; + } MITK_INFO << "Handling results..."; auto newNode = mitk::DataNode::New(); newNode->SetData(image); newNode->SetName(m_OldNodeName + nameExtension); // 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); EnableControls(); // update rendering mitk::RenderingManager::GetInstance()->InitializeViews(image->GetGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); MITK_INFO << "Handling results...[Done]"; } 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) { 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(); DisableControls(); BmodeThread *thread = new BmodeThread(); connect(thread, &BmodeThread::result, this, &PAImageProcessing::HandleResults); connect(thread, &BmodeThread::finished, thread, &QObject::deleteLater); bool useGPU = m_Controls.UseGPUBmode->isChecked(); if (m_Controls.BModeMethod->currentText() == "Absolute Filter") thread->setConfig(m_UseLogfilter, m_ResampleSpacing, mitk::PhotoacousticFilterService::BModeMethod::Abs, useGPU); else if (m_Controls.BModeMethod->currentText() == "Envelope Detection") thread->setConfig(m_UseLogfilter, m_ResampleSpacing, mitk::PhotoacousticFilterService::BModeMethod::EnvelopeDetection, useGPU); thread->setInputImage(image); thread->setFilterBank(m_FilterBank); MITK_INFO << "Started new thread for Image Processing"; thread->start(); } } } void PAImageProcessing::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) { 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(); DisableControls(); CropThread *thread = new CropThread(); connect(thread, &CropThread::result, this, &PAImageProcessing::HandleResults); connect(thread, &CropThread::finished, thread, &QObject::deleteLater); if(m_Controls.Partial->isChecked()) thread->setConfig(m_Controls.CutoffAbove->value(), m_Controls.CutoffBelow->value(), m_Controls.boundLow->value(), m_Controls.boundHigh->value()); else 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::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 applying a bandpass filter."); 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) { auto config = CreateBeamformingSettings(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(); DisableControls(); BandpassThread *thread = new BandpassThread(); connect(thread, &BandpassThread::result, this, &PAImageProcessing::HandleResults); connect(thread, &BandpassThread::finished, thread, &QObject::deleteLater); float BPHighPass = 1000000.0f * m_Controls.BPhigh->value(); // [Now in Hz] float BPLowPass = 1000000.0f * m_Controls.BPlow->value(); // [Now in Hz] thread->setConfig(BPHighPass, BPLowPass, m_Controls.BPFalloffLow->value(), m_Controls.BPFalloffHigh->value(), config->GetTimeSpacing(), config->GetSpeedOfSound(), m_Controls.IsBFImage->isChecked()); thread->setInputImage(image); thread->setFilterBank(m_FilterBank); MITK_INFO << "Started new thread for Bandpass filter"; thread->start(); } } } 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); float speedOfSound = m_Controls.SpeedOfSound->value(); // [m/s] std::stringstream frequency; float timeSpacing; if (m_Controls.UseImageSpacing->isChecked()) { timeSpacing = image->GetGeometry()->GetSpacing()[1] / 1000000.0f; MITK_INFO << "Calculated Scan Depth of " << (image->GetDimension(1)*image->GetGeometry()->GetSpacing()[1] / 1000000) * speedOfSound * 100 / 2 << "cm"; } else { timeSpacing = (2 * m_Controls.ScanDepth->value() / 1000 / speedOfSound) / image->GetDimension(1); } float maxFrequency = (1 / timeSpacing) / 2; if(m_Controls.IsBFImage->isChecked()) maxFrequency = ( 1 / (image->GetGeometry()->GetSpacing()[1] / 1e3 / speedOfSound)) / 2; frequency << maxFrequency / 1e6; //[MHz] frequency << "MHz"; m_Controls.BPhigh->setMaximum(maxFrequency / 1e6); m_Controls.BPlow->setMaximum(maxFrequency / 1e6); 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(); } mitk::BeamformingSettings::Pointer PAImageProcessing::CreateBeamformingSettings(mitk::Image::Pointer image) { mitk::BeamformingSettings::BeamformingAlgorithm algorithm = mitk::BeamformingSettings::BeamformingAlgorithm::DAS; if ("DAS" == m_Controls.BFAlgorithm->currentText()) algorithm = mitk::BeamformingSettings::BeamformingAlgorithm::DAS; else if ("DMAS" == m_Controls.BFAlgorithm->currentText()) algorithm = mitk::BeamformingSettings::BeamformingAlgorithm::DMAS; else if ("sDMAS" == m_Controls.BFAlgorithm->currentText()) algorithm = mitk::BeamformingSettings::BeamformingAlgorithm::sDMAS; mitk::BeamformingSettings::DelayCalc delay = mitk::BeamformingSettings::DelayCalc::Spherical; mitk::BeamformingSettings::Apodization apod = mitk::BeamformingSettings::Apodization::Box; if ("Von Hann" == m_Controls.Apodization->currentText()) { apod = mitk::BeamformingSettings::Apodization::Hann; } else if ("Hamming" == m_Controls.Apodization->currentText()) { apod = mitk::BeamformingSettings::Apodization::Hamm; } else if ("Box" == m_Controls.Apodization->currentText()) { apod = mitk::BeamformingSettings::Apodization::Box; } float pitchInMeters = m_Controls.Pitch->value() / 1000; // [m] float speedOfSound = m_Controls.SpeedOfSound->value(); // [m/s] unsigned int samplesPerLine = m_Controls.Samples->value(); unsigned int reconstructionLines = m_Controls.Lines->value(); unsigned int apodizatonArraySize = m_Controls.Lines->value(); float angle = m_Controls.Angle->value(); // [deg] bool useGPU = m_Controls.UseGPUBf->isChecked(); float timeSpacing; if (m_Controls.UseImageSpacing->isChecked()) { timeSpacing = image->GetGeometry()->GetSpacing()[1] / 1000000.0f; MITK_INFO << "Calculated Scan Depth of " << (image->GetDimension(1)*image->GetGeometry()->GetSpacing()[1] / 1000000) * speedOfSound * 100 / 2 << "cm"; } else { timeSpacing = (2 * m_Controls.ScanDepth->value() / 1000 / speedOfSound) / image->GetDimension(1); } bool isPAImage = true; if ("US Image" == m_Controls.ImageType->currentText()) { isPAImage = false; } else if ("PA Image" == m_Controls.ImageType->currentText()) { isPAImage = true; } float reconstructionDepth = m_Controls.ReconstructionDepth->value() / 1000.f; // [m] return mitk::BeamformingSettings::New(pitchInMeters, speedOfSound, timeSpacing, angle, isPAImage, samplesPerLine, reconstructionLines, image->GetDimensions(), reconstructionDepth, useGPU, 16, delay, apod, apodizatonArraySize, algorithm); } void PAImageProcessing::EnableControls() { m_Controls.BatchProcessing->setEnabled(true); m_Controls.StepBeamforming->setEnabled(true); m_Controls.StepBandpass->setEnabled(true); m_Controls.StepCropping->setEnabled(true); m_Controls.StepBMode->setEnabled(true); UpdateSaveBoxes(); m_Controls.DoResampling->setEnabled(true); UseResampling(); m_Controls.Logfilter->setEnabled(true); m_Controls.BModeMethod->setEnabled(true); m_Controls.buttonApplyBModeFilter->setEnabled(true); m_Controls.CutoffAbove->setEnabled(true); m_Controls.CutoffBelow->setEnabled(true); m_Controls.buttonApplyCropFilter->setEnabled(true); m_Controls.BPSpeedOfSound->setEnabled(true); m_Controls.buttonApplyBandpass->setEnabled(true); m_Controls.Partial->setEnabled(true); m_Controls.boundHigh->setEnabled(true); m_Controls.boundLow->setEnabled(true); m_Controls.BFAlgorithm->setEnabled(true); m_Controls.ReconstructionDepth->setEnabled(true); m_Controls.ImageType->setEnabled(true); m_Controls.Apodization->setEnabled(true); #ifdef PHOTOACOUSTICS_USE_GPU m_Controls.UseGPUBf->setEnabled(true); m_Controls.UseGPUBmode->setEnabled(true); #endif m_Controls.BPhigh->setEnabled(true); m_Controls.BPlow->setEnabled(true); m_Controls.BPFalloffLow->setEnabled(true); m_Controls.BPFalloffHigh->setEnabled(true); m_Controls.UseImageSpacing->setEnabled(true); UseImageSpacing(); m_Controls.Pitch->setEnabled(true); m_Controls.ElementCount->setEnabled(true); m_Controls.SpeedOfSound->setEnabled(true); m_Controls.Samples->setEnabled(true); m_Controls.Lines->setEnabled(true); m_Controls.Angle->setEnabled(true); m_Controls.buttonApplyBeamforming->setEnabled(true); m_Controls.UseSignalDelay->setEnabled(true); m_Controls.SignalDelay->setEnabled(true); } void PAImageProcessing::DisableControls() { m_Controls.BatchProcessing->setEnabled(false); m_Controls.StepBeamforming->setEnabled(false); m_Controls.StepBandpass->setEnabled(false); m_Controls.StepCropping->setEnabled(false); m_Controls.StepBMode->setEnabled(false); m_Controls.SaveBeamforming->setEnabled(false); m_Controls.SaveBandpass->setEnabled(false); m_Controls.SaveCropping->setEnabled(false); m_Controls.SaveBMode->setEnabled(false); m_Controls.DoResampling->setEnabled(false); m_Controls.ResamplingValue->setEnabled(false); m_Controls.Logfilter->setEnabled(false); m_Controls.BModeMethod->setEnabled(false); m_Controls.buttonApplyBModeFilter->setEnabled(false); m_Controls.CutoffAbove->setEnabled(false); m_Controls.CutoffBelow->setEnabled(false); m_Controls.buttonApplyCropFilter->setEnabled(false); m_Controls.BPSpeedOfSound->setEnabled(false); m_Controls.buttonApplyBandpass->setEnabled(false); m_Controls.Partial->setEnabled(false); m_Controls.boundHigh->setEnabled(false); m_Controls.boundLow->setEnabled(false); m_Controls.BFAlgorithm->setEnabled(false); m_Controls.ReconstructionDepth->setEnabled(false); m_Controls.ImageType->setEnabled(false); m_Controls.Apodization->setEnabled(false); #ifdef PHOTOACOUSTICS_USE_GPU m_Controls.UseGPUBf->setEnabled(false); m_Controls.UseGPUBmode->setEnabled(false); #endif m_Controls.BPhigh->setEnabled(false); m_Controls.BPlow->setEnabled(false); m_Controls.BPFalloffLow->setEnabled(false); m_Controls.BPFalloffHigh->setEnabled(false); m_Controls.UseImageSpacing->setEnabled(false); m_Controls.ScanDepth->setEnabled(false); m_Controls.Pitch->setEnabled(false); m_Controls.ElementCount->setEnabled(false); m_Controls.SpeedOfSound->setEnabled(false); m_Controls.Samples->setEnabled(false); m_Controls.Lines->setEnabled(false); m_Controls.Angle->setEnabled(false); m_Controls.buttonApplyBeamforming->setEnabled(false); m_Controls.UseSignalDelay->setEnabled(false); m_Controls.SignalDelay->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 preprocessedImage = m_InputImage; if (m_SignalDelay != 0) { int cropPixels = std::round(m_SignalDelay / m_BFconfig->GetTimeSpacing() / 1000000); MITK_INFO << cropPixels; - preprocessedImage = m_FilterBank->ApplyCropping(m_InputImage, cropPixels, 0, 0, 0, 0, m_InputImage->GetDimension(2) - 1); + int errCode = 0; + m_InputImage = m_FilterBank->ApplyCropping(m_InputImage, cropPixels, 0, 0, 0, 0, 0, &errCode); + + m_BFconfig = mitk::BeamformingSettings::New(m_BFconfig->GetPitchInMeters(), m_BFconfig->GetSpeedOfSound(), + m_BFconfig->GetTimeSpacing(), m_BFconfig->GetAngle(), m_BFconfig->GetIsPhotoacousticImage(), m_BFconfig->GetSamplesPerLine(), + m_BFconfig->GetReconstructionLines(), m_InputImage->GetDimensions(), m_BFconfig->GetReconstructionDepth(), + m_BFconfig->GetUseGPU(), m_BFconfig->GetGPUBatchSize(), m_BFconfig->GetDelayCalculationMethod(), m_BFconfig->GetApod(), + m_BFconfig->GetApodizationArraySize(), m_BFconfig->GetAlgorithm()); } - m_BFconfig = mitk::BeamformingSettings::New(m_BFconfig->GetPitchInMeters(), m_BFconfig->GetSpeedOfSound(), - m_BFconfig->GetTimeSpacing(), m_BFconfig->GetAngle(), m_BFconfig->GetIsPhotoacousticImage(), m_BFconfig->GetSamplesPerLine(), - m_BFconfig->GetReconstructionLines(), preprocessedImage->GetDimensions(), m_BFconfig->GetReconstructionDepth(), - m_BFconfig->GetUseGPU(), m_BFconfig->GetGPUBatchSize(), m_BFconfig->GetDelayCalculationMethod(), m_BFconfig->GetApod(), - m_BFconfig->GetApodizationArraySize(), m_BFconfig->GetAlgorithm()); - mitk::Image::Pointer resultImage; std::function progressHandle = [this](int progress, std::string progressInfo) { emit updateProgress(progress, progressInfo); }; - resultImage = m_FilterBank->ApplyBeamforming(preprocessedImage, m_BFconfig, progressHandle); + resultImage = m_FilterBank->ApplyBeamforming(m_InputImage, m_BFconfig, progressHandle); emit result(resultImage, "_bf"); } void BeamformingThread::setConfig(mitk::BeamformingSettings::Pointer BFconfig) { m_BFconfig = BFconfig; } void BeamformingThread::setSignalDelay(float delay) { m_SignalDelay = delay; } void BeamformingThread::setInputImage(mitk::Image::Pointer image) { m_InputImage = image; } void BmodeThread::run() { mitk::Image::Pointer resultImage = m_FilterBank->ApplyBmodeFilter(m_InputImage, m_Method, m_UseLogfilter); if (m_ResampleSpacing != 0) { double desiredSpacing[2]{ m_InputImage->GetGeometry()->GetSpacing()[0], m_ResampleSpacing }; resultImage = m_FilterBank->ApplyResampling(resultImage, desiredSpacing); } emit result(resultImage, "_bmode"); } void BmodeThread::setConfig(bool useLogfilter, double resampleSpacing, mitk::PhotoacousticFilterService::BModeMethod method, bool useGPU) { m_UseLogfilter = useLogfilter; m_ResampleSpacing = resampleSpacing; m_Method = method; m_UseGPU = useGPU; } void BmodeThread::setInputImage(mitk::Image::Pointer image) { m_InputImage = image; } void CropThread::run() { mitk::Image::Pointer resultImage; - resultImage = m_FilterBank->ApplyCropping(m_InputImage, m_CutAbove, m_CutBelow, 0, 0, m_CutSliceFirst, (m_InputImage->GetDimension(2) - 1) - m_CutSliceLast); + + int errCode = 0; + + resultImage = m_FilterBank->ApplyCropping(m_InputImage, m_CutAbove, m_CutBelow, 0, 0, m_CutSliceFirst, (m_InputImage->GetDimension(2) - 1) - m_CutSliceLast, &errCode); + if (errCode == -1) + { + emit result(nullptr, "_cropped"); + return; + } emit result(resultImage, "_cropped"); } 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 = m_FilterBank->ApplyBandpassFilter(m_InputImage, m_BPHighPass, m_BPLowPass, m_TukeyAlphaHighPass, m_TukeyAlphaLowPass, m_TimeSpacing, m_SpeedOfSound, m_IsBFImage); emit result(resultImage, "_bandpassed"); } void BandpassThread::setConfig(float BPHighPass, float BPLowPass, float TukeyAlphaHighPass, float TukeyAlphaLowPass, float TimeSpacing, float SpeedOfSound, bool IsBFImage) { m_BPHighPass = BPHighPass; m_BPLowPass = BPLowPass; m_TukeyAlphaHighPass = TukeyAlphaHighPass; m_TukeyAlphaLowPass = TukeyAlphaLowPass; m_TimeSpacing = TimeSpacing; m_SpeedOfSound = SpeedOfSound; m_IsBFImage = IsBFImage; } void BandpassThread::setInputImage(mitk::Image::Pointer image) { m_InputImage = image; }