diff --git a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASDevice.cpp b/Modules/US/USHardwareDiPhAS/mitkUSDiPhASDevice.cpp index 5cb68f1dcd..ed9942b062 100644 --- a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASDevice.cpp +++ b/Modules/US/USHardwareDiPhAS/mitkUSDiPhASDevice.cpp @@ -1,307 +1,308 @@ /*=================================================================== 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 "mitkUSDiPhASDevice.h" #include "mitkUSDiPhASCustomControls.h" mitk::USDiPhASDevice::USDiPhASDevice(std::string manufacturer, std::string model) : mitk::USDevice(manufacturer, model), m_ControlsProbes(mitk::USDiPhASProbesControls::New(this)), m_ImageSource(mitk::USDiPhASImageSource::New(this)), m_ControlInterfaceCustom(mitk::USDiPhASCustomControls::New(this)), m_IsRunning(false), m_BurstHalfwaveClockCount(7), m_Interleaved(true) { m_NumberOfOutputs = 2; this->SetNumberOfIndexedOutputs(m_NumberOfOutputs); SetNthOutput(0, this->MakeOutput(0)); SetNthOutput(1, this->MakeOutput(1)); } mitk::USDiPhASDevice::~USDiPhASDevice() { + } //Gets std::string mitk::USDiPhASDevice::GetDeviceClass() { return "org.mitk.modules.us.USDiPhASDevice"; } mitk::USControlInterfaceProbes::Pointer mitk::USDiPhASDevice::GetControlInterfaceProbes() { return m_ControlsProbes.GetPointer(); }; mitk::USAbstractControlInterface::Pointer mitk::USDiPhASDevice::GetControlInterfaceCustom() { return m_ControlInterfaceCustom.GetPointer(); } mitk::USImageSource::Pointer mitk::USDiPhASDevice::GetUSImageSource() { return m_ImageSource.GetPointer(); } ScanModeNative& mitk::USDiPhASDevice::GetScanMode() { return m_ScanMode; } // Setup and Cleanup bool mitk::USDiPhASDevice::OnInitialization() { return true; } //---------------------------------------------------------------------------------------------------------------------------- /* ugly wrapper stuff - find better solution so it isn't necessary to create a global pointer to USDiPhASDevice... * passing a lambda function would be nicer - sadly something goes wrong when passing the adress of a lambda function: * the API produces access violations. Passing the Lambda function itself would be preferable, but that's not possible */ mitk::USDiPhASDevice* w_device; mitk::USDiPhASImageSource* w_ISource; void WrapperMessageCallback(const char* message) { w_device->MessageCallback(message); } void WrapperImageDataCallback( short* rfDataChannelData, int channelDatalinesPerDataset, int channelDataSamplesPerChannel, int channelDataTotalDatasets, short* rfDataArrayBeamformed, int beamformedLines, int beamformedSamples, int beamformedTotalDatasets, unsigned char* imageData, int imageWidth, int imageHeight, int imagePixelFormat, int imageSetsTotal, double timeStamp) { w_ISource->ImageDataCallback( rfDataChannelData, channelDatalinesPerDataset, channelDataSamplesPerChannel, channelDataTotalDatasets, rfDataArrayBeamformed, beamformedLines, beamformedSamples, beamformedTotalDatasets, imageData, imageWidth, imageHeight, imagePixelFormat, imageSetsTotal, timeStamp); } //---------------------------------------------------------------------------------------------------------------------------- bool mitk::USDiPhASDevice::OnConnection() { w_device = this; w_ISource = m_ImageSource; // Need those pointers for the forwarders to call member functions; createBeamformer expects non-member function pointers. createBeamformer((StringMessageCallback)&WrapperMessageCallback, (NewDataCallback)&WrapperImageDataCallback); InitializeScanMode(); initBeamformer(); //start the hardware connection m_ImageSource->UpdateImageGeometry(); //make sure the image geometry is initialized! // pass the new scanmode to the device: setupScan(this->m_ScanMode); return true; } bool mitk::USDiPhASDevice::OnDisconnection() { //close the beamformer so hardware is disconnected closeBeamformer(); return true; } bool mitk::USDiPhASDevice::OnActivation() { // probe controls are available now m_ControlsProbes->SetIsActive(true); if (m_ControlsProbes->GetProbesCount() < 1) { MITK_WARN("USDevice")("USDiPhASDevice") << "No probe found."; return false; } m_ControlsProbes->SelectProbe(0); // toggle the beamformer of the API if(!m_IsRunning) m_IsRunning=toggleFreeze(); return true; } bool mitk::USDiPhASDevice::OnDeactivation() { if(m_IsRunning) m_IsRunning=toggleFreeze(); return true; } void mitk::USDiPhASDevice::OnFreeze(bool freeze) { if(m_IsRunning==freeze) m_IsRunning=toggleFreeze(); // toggleFreeze() returns true if it starts running the beamformer, otherwise false } void mitk::USDiPhASDevice::UpdateScanmode() { OnFreeze(true); SetInterleaved(m_Interleaved); // update the beamforming parameters... UpdateTransmitEvents(); if (!(dynamic_cast(this->m_ControlInterfaceCustom.GetPointer())->GetSilentUpdate())) { setupScan(this->m_ScanMode); m_ImageSource->UpdateImageGeometry(); } OnFreeze(false); } void mitk::USDiPhASDevice::UpdateTransmitEvents() { int numChannels = m_ScanMode.reconstructionLines; // transmitEventsCount defines only the number of acoustic measurements (angles); there will be one event added to the start for OA measurement m_ScanMode.TransmitEvents = new TransmitEventNative[m_ScanMode.transmitEventsCount]; for (int ev = 0; ev < m_ScanMode.transmitEventsCount; ++ev) { m_ScanMode.TransmitEvents[ev].transmitEventDelays = new float[numChannels]; m_ScanMode.TransmitEvents[ev].BurstHalfwaveClockCountPerChannel = new int[numChannels]; m_ScanMode.TransmitEvents[ev].BurstCountPerChannel = new int[numChannels]; m_ScanMode.TransmitEvents[ev].BurstUseNegativePolarityPerChannel = new bool[numChannels]; m_ScanMode.TransmitEvents[ev].ChannelMultiplexerSetups = nullptr; float tiltStrength = ((m_ScanMode.transmitEventsCount - 1) / 2 - ev) * 20e-9f; for (int i = 0; i < numChannels; ++i) { m_ScanMode.TransmitEvents[ev].BurstHalfwaveClockCountPerChannel[i] = m_BurstHalfwaveClockCount; // 120 MHz / (2 * (predefinedBurstHalfwaveClockCount + 1)) --> 7.5 MHz m_ScanMode.TransmitEvents[ev].BurstCountPerChannel[i] = 1; // Burst with 1 cycle m_ScanMode.TransmitEvents[ev].BurstUseNegativePolarityPerChannel[i] = true; m_ScanMode.TransmitEvents[ev].transmitEventDelays[i] = 2e-6f + (i - numChannels / 2) * tiltStrength; } } m_ScanMode.transmitSequenceCount = 1; m_ScanMode.transmitSequences = new SequenceNative[m_ScanMode.transmitSequenceCount]; m_ScanMode.transmitSequences[0].startEvent = 0; m_ScanMode.transmitSequences[0].endEvent = m_ScanMode.transmitEventsCount; } void mitk::USDiPhASDevice::InitializeScanMode() { // create a scanmode to be used for measurements: m_ScanMode.scanModeName = "InterleavedMode"; // configure a linear transducer m_ScanMode.transducerName = "L5-10"; m_ScanMode.transducerCurvedRadiusMeter = 0; m_ScanMode.transducerElementCount = 128; m_ScanMode.transducerFrequencyHz = 7500000; m_ScanMode.transducerPitchMeter = 0.0003f; m_ScanMode.transducerType = 1; // configure the receive paramters: m_ScanMode.receivePhaseLengthSeconds = 185e-6f; // about 15 cm imaging depth m_ScanMode.tgcdB = new unsigned char[8]; for (int tgc = 0; tgc < 8; ++tgc) m_ScanMode.tgcdB[tgc] = tgc * 2 + 10; m_ScanMode.accumulation = 1; m_ScanMode.bandpassApply = false; m_ScanMode.averagingCount = 1; // configure general processing: m_ScanMode.transferChannelData = true; // configure reconstruction processing: m_ScanMode.averageSpeedOfSound = 1540; m_ScanMode.computeBeamforming = true; // setup beamforming parameters: SetInterleaved(true); m_ScanMode.reconstructedLinePitchMmOrAngleDegree = 0.3f; m_ScanMode.reconstructionLines = 128; m_ScanMode.reconstructionSamplesPerLine = 2048; m_ScanMode.transferBeamformedData = true; // configure the transmit sequence(s): m_ScanMode.transmitEventsCount = 1; m_ScanMode.transmitPhaseLengthSeconds = 1e-6f; m_ScanMode.voltageV = 75; UpdateTransmitEvents(); // configure bandpass: m_ScanMode.bandpassApply = false; m_ScanMode.bandpassFrequencyLowHz = 1e6f; m_ScanMode.bandpassFrequencyHighHz = 20e6f; // configure image generation: m_ScanMode.imageWidth = 512; m_ScanMode.imageHeight = 512; m_ScanMode.imageMultiplier = 1; m_ScanMode.imageLeveling = 0; m_ScanMode.transferImageData = false; // Trigger setup: m_ScanMode.triggerSetup.enabled = true; m_ScanMode.triggerSetup.constantPulseRepetitionRateHz = 20; m_ScanMode.triggerSetup.triggerWidthMicroseconds = 15; m_ScanMode.triggerSetup.delayTrigger2Microseconds = 300; } // callback for the DiPhAS API void mitk::USDiPhASDevice::MessageCallback(const char* message) { MITK_INFO << "DiPhAS API: " << message << '\n'; } void mitk::USDiPhASDevice::SetBursts(int bursts) { m_BurstHalfwaveClockCount = bursts; } bool mitk::USDiPhASDevice::IsInterleaved() { return m_Interleaved; } void mitk::USDiPhASDevice::SetInterleaved(bool interleaved) { m_Interleaved = interleaved; if (interleaved) { m_ScanMode.scanModeName = "Interleaved Beamforming Mode"; m_CurrentBeamformingAlgorithm = Beamforming::Interleaved_OA_US; paramsInterleaved.SpeedOfSoundMeterPerSecond = m_ScanMode.averageSpeedOfSound; paramsInterleaved.angleSkipFactor = 1; paramsInterleaved.OptoacousticDelay = 0.0000003; // 300ns paramsInterleaved.filter = Filter::None; m_ScanMode.beamformingAlgorithmParameters = ¶msInterleaved; } else { m_ScanMode.scanModeName = "Plane Wave Beamforming Mode"; m_CurrentBeamformingAlgorithm = Beamforming::PlaneWaveCompound; paramsPlaneWave.SpeedOfSoundMeterPerSecond = m_ScanMode.averageSpeedOfSound; paramsPlaneWave.angleSkipFactor = 0; paramsPlaneWave.usePhaseCoherence = 0; m_ScanMode.beamformingAlgorithmParameters = ¶msPlaneWave; } m_ScanMode.beamformingAlgorithm = m_CurrentBeamformingAlgorithm; } \ No newline at end of file diff --git a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASImageSource.cpp b/Modules/US/USHardwareDiPhAS/mitkUSDiPhASImageSource.cpp index 549ce8ef16..3866134eb4 100644 --- a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASImageSource.cpp +++ b/Modules/US/USHardwareDiPhAS/mitkUSDiPhASImageSource.cpp @@ -1,931 +1,931 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ // std dependencies #include #include #include // mitk dependencies #include "mitkUSDiPhASDevice.h" #include "mitkUSDiPhASImageSource.h" #include #include "mitkUSDiPhASBModeImageFilter.h" #include "ITKUltrasound/itkBModeImageFilter.h" #include "mitkImageCast.h" #include "mitkITKImageImport.h" // itk dependencies #include "itkImage.h" #include "itkResampleImageFilter.h" #include "itkCastImageFilter.h" #include "itkCropImageFilter.h" #include "itkRescaleIntensityImageFilter.h" #include "itkIntensityWindowingImageFilter.h" #include #include "itkMultiplyImageFilter.h" mitk::USDiPhASImageSource::USDiPhASImageSource(mitk::USDiPhASDevice* device) : m_Device(device), m_StartTime(((float)std::clock()) / CLOCKS_PER_SEC), m_UseGUIOutPut(false), m_DataType(DataType::Image_uChar), m_GUIOutput(nullptr), m_UseBModeFilter(false), m_CurrentlyRecording(false), m_DataTypeModified(true), m_DataTypeNext(DataType::Image_uChar), m_CurrentImageTimestamp(0), m_PyroConnected(false), m_ImageTimestampBuffer(), m_VerticalSpacing(0), m_UseBModeFilterModified(false), m_UseBModeFilterNext(false), m_ScatteringCoefficientModified(false), m_CompensateForScatteringModified(false), m_VerticalSpacingModified(false), m_ScatteringCoefficient(15), m_CompensateForScattering(false), m_CompensateEnergy(false), m_CompensateEnergyNext(false), m_CompensateEnergyModified(false) { m_BufferSize = 100; m_ImageTimestampBuffer.insert(m_ImageTimestampBuffer.begin(), m_BufferSize, 0); m_LastWrittenImage = m_BufferSize - 1; m_ImageBuffer.insert(m_ImageBuffer.begin(), m_BufferSize, nullptr); us::ModuleResource resourceFile; std::string name; m_FluenceCompOriginal.insert(m_FluenceCompOriginal.begin(), 5, Image::New()); for (int i = 5; i <= 25; ++i) { name = "c:\\HomogeneousScatteringAssumptions\\Scattering" + std::to_string(i) + ".nrrd"; m_FluenceCompOriginal.push_back(mitk::IOUtil::LoadImage(name)); } m_FluenceCompResized.insert(m_FluenceCompResized.begin(), 26, Image::New()); m_FluenceCompResizedItk.insert(m_FluenceCompResizedItk.begin(), 26, itk::Image::New()); } mitk::USDiPhASImageSource::~USDiPhASImageSource() { // close the pyro MITK_INFO("Pyro Debug") << "StopDataAcquisition: " << m_Pyro->StopDataAcquisition(); MITK_INFO("Pyro Debug") << "CloseConnection: " << m_Pyro->CloseConnection(); m_PyroConnected = false; m_Pyro = nullptr; } void mitk::USDiPhASImageSource::GetNextRawImage(std::vector& imageVector) { // modify all settings that have been changed here, so we don't get multithreading issues if (m_DataTypeModified) { SetDataType(m_DataTypeNext); m_DataTypeModified = false; UpdateImageGeometry(); } if (m_UseBModeFilterModified) { SetUseBModeFilter(m_UseBModeFilterNext); m_UseBModeFilterModified = false; } if (m_VerticalSpacingModified) { m_VerticalSpacing = m_VerticalSpacingNext; m_VerticalSpacingModified = false; } if (m_ScatteringCoefficientModified) { m_ScatteringCoefficient = m_ScatteringCoefficientNext; m_ScatteringCoefficientModified = false; } if (m_CompensateForScatteringModified) { m_CompensateForScattering = m_CompensateForScatteringNext; m_CompensateForScatteringModified = false; } if (m_CompensateEnergyModified) { m_CompensateEnergy = m_CompensateEnergyNext; m_CompensateEnergyModified = false; } if (imageVector.size() != 2) { imageVector.resize(2); } // make sure image is nullptr mitk::Image::Pointer image = nullptr; float ImageEnergyValue = 0; for (int i = 100; i > 90 && ImageEnergyValue <= 0; --i) { if (m_ImageTimestampBuffer[(m_LastWrittenImage + i) % 100] != 0) { ImageEnergyValue = m_Pyro->GetClosestEnergyInmJ(m_ImageTimestampBuffer[(m_LastWrittenImage + i) % 100]); if (ImageEnergyValue > 0) { image = &(*m_ImageBuffer[(m_LastWrittenImage + i) % 100]); } } } // if we did not get any usable Energy value, compensate using this default value if (image == nullptr) { image = &(*m_ImageBuffer[m_LastWrittenImage]); ImageEnergyValue = 40; if (image == nullptr) return; } // do image processing before displaying it if (image.IsNotNull()) { itkFloatImageType::Pointer itkImage; mitk::CastToItkImage(image, itkImage); image = mitk::GrabItkImageMemory(itkImage); //thereby using float images image = CutOffTop(image, 165); // now apply filters to the image, if the options have been selected. if ((m_CompensateForScattering || m_UseBModeFilter) && m_DataType == DataType::Beamformed_Short) { if (m_Device->GetScanMode().beamformingAlgorithm == Beamforming::PlaneWaveCompound) // this is for ultrasound only mode { if (m_UseBModeFilter) { image = ApplyBmodeFilter(image, true); if (m_VerticalSpacing) image = ResampleOutputVertical(image, m_VerticalSpacing); } } else { Image::Pointer imagePA = Image::New(); unsigned int dim[] = { image->GetDimension(0),image->GetDimension(1),1}; imagePA->Initialize(image->GetPixelType(), 3, dim); imagePA->SetGeometry(image->GetGeometry()); Image::Pointer imageUS = Image::New(); imageUS->Initialize(image->GetPixelType(), 3, dim); imageUS->SetGeometry(image->GetGeometry()); ImageReadAccessor inputReadAccessorCopyPA(image, image->GetSliceData(0)); imagePA->SetSlice(inputReadAccessorCopyPA.GetData(), 0); ImageReadAccessor inputReadAccessorCopyUS(image, image->GetSliceData(1)); imageUS->SetSlice(inputReadAccessorCopyUS.GetData(), 0); // first, seperate the PA image from the USImages // then, we compensate the PAImage using our ImageEnergyValue if(m_CompensateEnergy) imagePA = MultiplyImage(imagePA, 1/ImageEnergyValue); // TODO: add the correct prefactor here!!!! // now we apply the BModeFilter if (m_UseBModeFilter) { imageUS = ApplyBmodeFilter(imageUS, true); // the US Images get a logarithmic filter imagePA = ApplyBmodeFilter(imagePA, false); } ImageReadAccessor inputReadAccessorPA(imagePA, imagePA->GetSliceData(0)); image->SetSlice(inputReadAccessorPA.GetData(), 0); ImageReadAccessor inputReadAccessorUS(imageUS, imageUS->GetSliceData(0)); image->SetSlice(inputReadAccessorUS.GetData(), 1); if (m_VerticalSpacing) { image = ResampleOutputVertical(image, m_VerticalSpacing); } // and finally the scattering corrections if (m_CompensateForScattering) { auto curResizeImage = m_FluenceCompResized.at(m_ScatteringCoefficient); // just for convenience // update the fluence reference images! bool doResampling = image->GetDimension(0) != curResizeImage->GetDimension(0) || image->GetDimension(1) != curResizeImage->GetDimension(1) || image->GetGeometry()->GetSpacing()[0] != curResizeImage->GetGeometry()->GetSpacing()[0] || image->GetGeometry()->GetSpacing()[1] != curResizeImage->GetGeometry()->GetSpacing()[1]; if (doResampling) { curResizeImage = ApplyResampling(m_FluenceCompOriginal.at(m_ScatteringCoefficient), image->GetGeometry()->GetSpacing(), image->GetDimensions()); double* rawOutputData = new double[image->GetDimension(0)*image->GetDimension(1)]; double* rawScatteringData = (double*)curResizeImage->GetData(); int sizeRawScatteringData = curResizeImage->GetDimension(0) * curResizeImage->GetDimension(1); int imageSize = image->GetDimension(0)*image->GetDimension(1); //everything above 1.5mm is still inside the transducer; therefore the fluence compensation image has to be positioned a little lower float upperCutoffmm = 1.5; int lowerBound = std::round(upperCutoffmm / image->GetGeometry()->GetSpacing()[1])*image->GetDimension(0); int upperBound = lowerBound + sizeRawScatteringData; for (int i = 0; i < lowerBound && i < imageSize; ++i) { rawOutputData[i] = 0; // everything than cannot be compensated shall be treated as garbage, here the upper 0.15mm } for (int i = lowerBound; i < upperBound && i < imageSize; ++i) { rawOutputData[i] = 1 / rawScatteringData[i-lowerBound]; } for (int i = upperBound; i < imageSize; ++i) { rawOutputData[i] = 0; // everything than cannot be compensated shall be treated as garbage } unsigned int dim[] = { image->GetDimension(0), image->GetDimension(1), 1 }; curResizeImage->Initialize(mitk::MakeScalarPixelType(), 3, dim); curResizeImage->SetGeometry(image->GetGeometry()); curResizeImage->SetSlice(rawOutputData,0); delete[] rawOutputData; mitk::CastToItkImage(curResizeImage, m_FluenceCompResizedItk.at(m_ScatteringCoefficient)); m_FluenceCompResized.at(m_ScatteringCoefficient) = mitk::GrabItkImageMemory(m_FluenceCompResizedItk.at(m_ScatteringCoefficient)); MITK_INFO << "Resized a fluence image."; } // actually apply the scattering compensation imagePA = ApplyScatteringCompensation(imagePA, m_ScatteringCoefficient); ImageReadAccessor inputReadAccessorPA(imagePA, imagePA->GetSliceData(0)); image->SetSlice(inputReadAccessorPA.GetData(), 0); } } } //TODO: completely rewrite this mess imageVector[0] = Image::New(); unsigned int dim[] = { image->GetDimension(0),image->GetDimension(1),1 }; imageVector[0]->Initialize(image->GetPixelType(), 3, dim); imageVector[0]->SetGeometry(image->GetGeometry()); imageVector[1] = Image::New(); imageVector[1]->Initialize(image->GetPixelType(), 3, dim); imageVector[1]->SetGeometry(image->GetGeometry()); ImageReadAccessor inputReadAccessorCopyPA(image, image->GetSliceData(0)); imageVector[0]->SetSlice(inputReadAccessorCopyPA.GetData(), 0); ImageReadAccessor inputReadAccessorCopyUS(image, image->GetSliceData(1)); imageVector[1]->SetSlice(inputReadAccessorCopyUS.GetData(), 0); } } mitk::Image::Pointer mitk::USDiPhASImageSource::ApplyBmodeFilter(mitk::Image::Pointer image, bool useLogFilter) { // we use this seperate ApplyBmodeFilter Method for processing of two-dimensional images // the image needs to be of floating point type for the envelope filter to work; the casting is done automatically by the CastToItkImage typedef itk::BModeImageFilter < itkFloatImageType, itkFloatImageType > BModeFilterType; BModeFilterType::Pointer bModeFilter = BModeFilterType::New(); // LogFilter typedef itk::PhotoacousticBModeImageFilter < itkFloatImageType, itkFloatImageType > PhotoacousticBModeImageFilter; PhotoacousticBModeImageFilter::Pointer photoacousticBModeFilter = PhotoacousticBModeImageFilter::New(); // No LogFilter itkFloatImageType::Pointer itkImage; itkFloatImageType::Pointer bmode; mitk::CastToItkImage(image, itkImage); if (useLogFilter) { bModeFilter->SetInput(itkImage); bModeFilter->SetDirection(1); bmode = bModeFilter->GetOutput(); } else { photoacousticBModeFilter->SetInput(itkImage); photoacousticBModeFilter->SetDirection(1); bmode = photoacousticBModeFilter->GetOutput(); } return mitk::GrabItkImageMemory(bmode); } mitk::Image::Pointer mitk::USDiPhASImageSource::CutOffTop(mitk::Image::Pointer image, int cutOffSize) { typedef itk::CropImageFilter < itkFloatImageType, itkFloatImageType > CutImageFilter; itkFloatImageType::SizeType cropSize; itkFloatImageType::Pointer itkImage; mitk::CastToItkImage(image, itkImage); cropSize[0] = 0; if(itkImage->GetLargestPossibleRegion().GetSize()[1] == 2048) cropSize[1] = cutOffSize; else cropSize[1] = 0; cropSize[2] = 0; CutImageFilter::Pointer cutOffFilter = CutImageFilter::New(); cutOffFilter->SetInput(itkImage); cutOffFilter->SetLowerBoundaryCropSize(cropSize); cutOffFilter->UpdateLargestPossibleRegion(); return mitk::GrabItkImageMemory(cutOffFilter->GetOutput()); } mitk::Image::Pointer mitk::USDiPhASImageSource::ResampleOutputVertical(mitk::Image::Pointer image, float verticalSpacing) { typedef itk::ResampleImageFilter < itkFloatImageType, itkFloatImageType > ResampleImageFilter; ResampleImageFilter::Pointer resampleImageFilter = ResampleImageFilter::New(); itkFloatImageType::Pointer itkImage; mitk::CastToItkImage(image, itkImage); itkFloatImageType::SpacingType outputSpacing; itkFloatImageType::SizeType inputSize = itkImage->GetLargestPossibleRegion().GetSize(); itkFloatImageType::SizeType outputSize = inputSize; outputSpacing[0] = itkImage->GetSpacing()[0] * (static_cast(inputSize[0]) / static_cast(outputSize[0])); outputSpacing[1] = verticalSpacing; outputSpacing[2] = itkImage->GetSpacing()[2]; outputSize[1] = inputSize[1] * itkImage->GetSpacing()[1] / outputSpacing[1]; typedef itk::IdentityTransform TransformType; resampleImageFilter->SetInput(itkImage); resampleImageFilter->SetSize(outputSize); - resampleImageFilter->SetOutputSpacing(outputSpacing); - resampleImageFilter->SetTransform(TransformType::New()); +resampleImageFilter->SetOutputSpacing(outputSpacing); +resampleImageFilter->SetTransform(TransformType::New()); - resampleImageFilter->UpdateLargestPossibleRegion(); - return mitk::GrabItkImageMemory(resampleImageFilter->GetOutput()); +resampleImageFilter->UpdateLargestPossibleRegion(); +return mitk::GrabItkImageMemory(resampleImageFilter->GetOutput()); } mitk::Image::Pointer mitk::USDiPhASImageSource::ApplyScatteringCompensation(mitk::Image::Pointer inputImage, int scattering) { typedef itk::MultiplyImageFilter MultiplyImageFilterType; itkFloatImageType::Pointer itkImage; mitk::CastToItkImage(inputImage, itkImage); MultiplyImageFilterType::Pointer multiplyFilter = MultiplyImageFilterType::New(); multiplyFilter->SetInput1(itkImage); multiplyFilter->SetInput2(m_FluenceCompResizedItk.at(m_ScatteringCoefficient)); return mitk::GrabItkImageMemory(multiplyFilter->GetOutput()); } mitk::Image::Pointer mitk::USDiPhASImageSource::ApplyResampling(mitk::Image::Pointer inputImage, mitk::Vector3D outputSpacing, unsigned int outputSize[3]) { typedef itk::ResampleImageFilter < itkFloatImageType, itkFloatImageType > ResampleImageFilter; ResampleImageFilter::Pointer resampleImageFilter = ResampleImageFilter::New(); itkFloatImageType::Pointer itkImage; mitk::CastToItkImage(inputImage, itkImage); itkFloatImageType::SpacingType outputSpacingItk; itkFloatImageType::SizeType inputSizeItk = itkImage->GetLargestPossibleRegion().GetSize(); itkFloatImageType::SizeType outputSizeItk = inputSizeItk; itkFloatImageType::SpacingType inputSpacing = itkImage->GetSpacing(); outputSizeItk[0] = outputSize[0]; - outputSizeItk[1] = 10*(inputSpacing[1] * inputSizeItk[1]) / (outputSpacing[1]); + outputSizeItk[1] = 10 * (inputSpacing[1] * inputSizeItk[1]) / (outputSpacing[1]); outputSizeItk[2] = 1; outputSpacingItk[0] = 0.996 * inputSpacing[0] * (static_cast(inputSizeItk[0]) / static_cast(outputSizeItk[0])); // TODO: find out why the spacing is not correct, so we need that factor; ?!?! outputSpacingItk[1] = inputSpacing[1] * (static_cast(inputSizeItk[1]) / static_cast(outputSizeItk[1])); outputSpacingItk[2] = outputSpacing[2]; typedef itk::IdentityTransform TransformType; resampleImageFilter->SetInput(itkImage); resampleImageFilter->SetSize(outputSizeItk); resampleImageFilter->SetOutputSpacing(outputSpacingItk); resampleImageFilter->SetTransform(TransformType::New()); resampleImageFilter->UpdateLargestPossibleRegion(); return mitk::GrabItkImageMemory(resampleImageFilter->GetOutput()); } mitk::Image::Pointer mitk::USDiPhASImageSource::MultiplyImage(mitk::Image::Pointer inputImage, double value) { typedef itk::MultiplyImageFilter MultiplyImageFilterType; itkFloatImageType::Pointer itkImage; mitk::CastToItkImage(inputImage, itkImage); MultiplyImageFilterType::Pointer multiplyFilter = MultiplyImageFilterType::New(); multiplyFilter->SetInput1(itkImage); multiplyFilter->SetConstant(value); return mitk::GrabItkImageMemory(multiplyFilter->GetOutput()); } void mitk::USDiPhASImageSource::ImageDataCallback( - short* rfDataChannelData, - int& channelDataChannelsPerDataset, - int& channelDataSamplesPerChannel, - int& channelDataTotalDatasets, - - short* rfDataArrayBeamformed, - int& beamformedLines, - int& beamformedSamples, - int& beamformedTotalDatasets, - - unsigned char* imageData, - int& imageWidth, - int& imageHeight, - int& imageBytesPerPixel, - int& imageSetsTotal, - - double& timeStamp) + short* rfDataChannelData, + int& channelDataChannelsPerDataset, + int& channelDataSamplesPerChannel, + int& channelDataTotalDatasets, + + short* rfDataArrayBeamformed, + int& beamformedLines, + int& beamformedSamples, + int& beamformedTotalDatasets, + + unsigned char* imageData, + int& imageWidth, + int& imageHeight, + int& imageBytesPerPixel, + int& imageSetsTotal, + + double& timeStamp) { if (m_DataTypeModified) return; if (!m_PyroConnected) { m_Pyro = mitk::OphirPyro::New(); MITK_INFO << "[Pyro Debug] OpenConnection: " << m_Pyro->OpenConnection(); MITK_INFO << "[Pyro Debug] StartDataAcquisition: " << m_Pyro->StartDataAcquisition(); m_PyroConnected = true; } bool writeImage = ((m_DataType == DataType::Image_uChar) && (imageData != nullptr)) || ((m_DataType == DataType::Beamformed_Short) && (rfDataArrayBeamformed != nullptr)); if (writeImage) { //get the timestamp we might save later on m_CurrentImageTimestamp = std::chrono::high_resolution_clock::now().time_since_epoch().count(); // create a new image and initialize it mitk::Image::Pointer image = mitk::Image::New(); switch (m_DataType) { case DataType::Image_uChar: { m_ImageDimensions[0] = imageWidth; m_ImageDimensions[1] = imageHeight; m_ImageDimensions[2] = imageSetsTotal; image->Initialize(mitk::MakeScalarPixelType(), 3, m_ImageDimensions); break; } case DataType::Beamformed_Short: { m_ImageDimensions[0] = beamformedLines; m_ImageDimensions[1] = beamformedSamples; m_ImageDimensions[2] = beamformedTotalDatasets; image->Initialize(mitk::MakeScalarPixelType(), 3, m_ImageDimensions); break; } } image->GetGeometry()->SetSpacing(m_ImageSpacing); image->GetGeometry()->Modified(); // write the given buffer into the image switch (m_DataType) { case DataType::Image_uChar: { for (unsigned char i = 0; i < imageSetsTotal; i++) { image->SetSlice(&imageData[i*imageHeight*imageWidth], i); } break; } case DataType::Beamformed_Short: { short* flipme = new short[beamformedLines*beamformedSamples*beamformedTotalDatasets]; int pixelsPerImage = beamformedLines*beamformedSamples; for (unsigned char currentSet = 0; currentSet < beamformedTotalDatasets; currentSet++) { for (unsigned short sample = 0; sample < beamformedSamples; sample++) { for (unsigned short line = 0; line < beamformedLines; line++) { flipme[sample*beamformedLines + line + pixelsPerImage*currentSet] = rfDataArrayBeamformed[line*beamformedSamples + sample + pixelsPerImage*currentSet]; } } // the beamformed pa image is flipped by 90 degrees; we need to flip it manually } for (unsigned char i = 0; i < beamformedTotalDatasets; i++) { image->SetSlice(&flipme[i*beamformedLines*beamformedSamples], i); // set every image to a different slice } delete[] flipme; break; } } if (m_SavingSettings.saveRaw && m_CurrentlyRecording && rfDataChannelData != nullptr) { unsigned int dim[3]; dim[0] = channelDataChannelsPerDataset; dim[1] = channelDataSamplesPerChannel; dim[2] = 1; short offset = m_Device->GetScanMode().accumulation * 2048; short* noOffset = new short[channelDataChannelsPerDataset*channelDataSamplesPerChannel*channelDataTotalDatasets]; for (unsigned char set = 0; set < 1; ++set)// channelDataTotalDatasets; ++set) // we ignore the raw US images for now { for (unsigned short sam = 0; sam < channelDataSamplesPerChannel; ++sam) { for (unsigned short chan = 0; chan < channelDataChannelsPerDataset; ++chan) { noOffset[set*channelDataSamplesPerChannel*channelDataChannelsPerDataset + sam * channelDataChannelsPerDataset + chan] = rfDataChannelData[set*channelDataSamplesPerChannel*channelDataChannelsPerDataset + sam * channelDataChannelsPerDataset + chan] - offset; // this offset in the raw Images is given by the API... } } } // save the raw images when recording for (unsigned char i = 0; i < 1; ++i)// channelDataTotalDatasets; ++i) // we ignore the raw US images for now { mitk::Image::Pointer rawImage = mitk::Image::New(); rawImage->Initialize(mitk::MakeScalarPixelType(), 3, dim); rawImage->SetSlice(&noOffset[i*channelDataChannelsPerDataset*channelDataSamplesPerChannel]); float& recordTime = m_Device->GetScanMode().receivePhaseLengthSeconds; int& speedOfSound = m_Device->GetScanMode().averageSpeedOfSound; mitk::Vector3D rawSpacing; rawSpacing[0] = m_Device->GetScanMode().transducerPitchMeter * 1000; // save in mm rawSpacing[1] = recordTime / channelDataSamplesPerChannel * 1000000; // save in us rawSpacing[2] = 1; rawImage->GetGeometry()->SetSpacing(rawSpacing); rawImage->GetGeometry()->Modified(); m_RawRecordedImages.push_back(rawImage); } delete[] noOffset; } itk::Index<3> pixel = { { (itk::Index<3>::IndexValueType)(image->GetDimension(0) / 2), (itk::Index<3>::IndexValueType)(22.0/532.0*m_Device->GetScanMode().reconstructionSamplesPerLine), 0 } }; //22/532*2048 = 84 if (!m_Pyro->IsSyncDelaySet() &&(image->GetPixelValueByIndex(pixel) < -30)) // #MagicNumber { MITK_INFO << "Setting SyncDelay now"; m_Pyro->SetSyncDelay(m_CurrentImageTimestamp); } m_ImageTimestampBuffer[(m_LastWrittenImage + 1) % m_BufferSize] = m_CurrentImageTimestamp; m_ImageBuffer[(m_LastWrittenImage + 1) % m_BufferSize] = image; m_LastWrittenImage = (m_LastWrittenImage + 1) % m_BufferSize; // if the user decides to start recording, we feed the vector the generated images if (m_CurrentlyRecording) { for (unsigned char index = 0; index < image->GetDimension(2); ++index) { if (image->IsSliceSet(index)) { m_RecordedImages.push_back(Image::New()); unsigned int dim[] = { image ->GetDimension(0), image->GetDimension(1), 1}; m_RecordedImages.back()->Initialize(image->GetPixelType(), 3, dim); m_RecordedImages.back()->SetGeometry(image->GetGeometry()); mitk::ImageReadAccessor inputReadAccessor(image, image->GetSliceData(index)); m_RecordedImages.back()->SetSlice(inputReadAccessor.GetData(),0); } } m_ImageTimestampRecord.push_back(m_CurrentImageTimestamp); // save timestamps for each laser image! } } } void mitk::USDiPhASImageSource::UpdateImageGeometry() { MITK_INFO << "Retreaving Image Geometry Information for Spacing..."; float& recordTime = m_Device->GetScanMode().receivePhaseLengthSeconds; int& speedOfSound = m_Device->GetScanMode().averageSpeedOfSound; float& pitch = m_Device->GetScanMode().reconstructedLinePitchMmOrAngleDegree; int& reconstructionLines = m_Device->GetScanMode().reconstructionLines; switch (m_DataType) { case DataType::Image_uChar : { int& imageWidth = m_Device->GetScanMode().imageWidth; int& imageHeight = m_Device->GetScanMode().imageHeight; m_ImageSpacing[0] = pitch * reconstructionLines / imageWidth; m_ImageSpacing[1] = recordTime * speedOfSound / 2 * 1000 / imageHeight; break; } case DataType::Beamformed_Short : { int& imageWidth = reconstructionLines; int& imageHeight = m_Device->GetScanMode().reconstructionSamplesPerLine; m_ImageSpacing[0] = pitch; m_ImageSpacing[1] = recordTime * speedOfSound / 2 * 1000 / imageHeight; break; } } m_ImageSpacing[2] = 1; MITK_INFO << "Retreaving Image Geometry Information for Spacing " << m_ImageSpacing[0] << " ... " << m_ImageSpacing[1] << " ... " << m_ImageSpacing[2] << " ...[DONE]"; } void mitk::USDiPhASImageSource::ModifyDataType(DataType dataT) { m_DataTypeModified = true; m_DataTypeNext = dataT; } void mitk::USDiPhASImageSource::ModifyUseBModeFilter(bool isSet) { m_UseBModeFilterModified = true; m_UseBModeFilterNext = isSet; } void mitk::USDiPhASImageSource::ModifyScatteringCoefficient(int coeff) { m_ScatteringCoefficientNext = coeff; m_ScatteringCoefficientModified = true; } void mitk::USDiPhASImageSource::ModifyCompensateForScattering(bool useIt) { m_CompensateForScatteringNext = useIt; m_CompensateForScatteringModified = true; } void mitk::USDiPhASImageSource::ModifyEnergyCompensation(bool compensate) { m_CompensateEnergyNext = compensate; m_CompensateEnergyModified = true; } void mitk::USDiPhASImageSource::SetDataType(DataType dataT) { if (dataT != m_DataType) { m_DataType = dataT; MITK_INFO << "Setting new DataType..." << dataT; switch (m_DataType) { case DataType::Image_uChar : MITK_INFO << "height: " << m_Device->GetScanMode().imageHeight << " width: " << m_Device->GetScanMode().imageWidth; break; case DataType::Beamformed_Short : MITK_INFO << "samples: " << m_Device->GetScanMode().reconstructionSamplesPerLine << " lines: " << m_Device->GetScanMode().reconstructionLines; break; } } } void mitk::USDiPhASImageSource::SetGUIOutput(std::function out) { USDiPhASImageSource::m_GUIOutput = out; m_StartTime = ((float)std::clock()) / CLOCKS_PER_SEC; //wait till the callback is available again m_UseGUIOutPut = false; } void mitk::USDiPhASImageSource::SetUseBModeFilter(bool isSet) { m_UseBModeFilter = isSet; } void mitk::USDiPhASImageSource::SetVerticalSpacing(float mm) { m_VerticalSpacingNext = mm; m_VerticalSpacingModified = true; } void mitk::USDiPhASImageSource::SetSavingSettings(SavingSettings settings) { m_SavingSettings = settings; } // this is just a little function to set the filenames below right inline void replaceAll(std::string& str, const std::string& from, const std::string& to) { if (from.empty()) return; size_t start_pos = 0; while ((start_pos = str.find(from, start_pos)) != std::string::npos) { str.replace(start_pos, from.length(), to); start_pos += to.length(); // In case 'to' contains 'from', like replacing 'x' with 'yx' } } void mitk::USDiPhASImageSource::SetRecordingStatus(bool record) { // start the recording process if (record) { m_RecordedImages.clear(); m_RawRecordedImages.clear(); // we make sure there are no leftovers m_ImageTimestampRecord.clear(); // also for the timestamps m_PixelValues.clear(); // aaaand for the pixel values if (m_SavingSettings.saveRaw) { m_Device->GetScanMode().transferChannelData = true; m_Device->UpdateScanmode(); // set the raw Data to be transfered } // tell the callback to start recording images m_CurrentlyRecording = true; } // save images, end recording, and clean up else { m_CurrentlyRecording = false; m_Device->GetScanMode().transferChannelData = false; // make sure raw Channel Data is not transferred anymore! m_Device->UpdateScanmode(); // get the time and date, put them into a nice string and create a folder for the images time_t time = std::time(nullptr); time_t* timeptr = &time; std::string currentDate = std::ctime(timeptr); replaceAll(currentDate, ":", "-"); currentDate.pop_back(); //std::string MakeFolder = "mkdir \"c:/DiPhASImageData/" + currentDate + "\""; //system(MakeFolder.c_str()); // initialize file paths and the images Image::Pointer PAImage = Image::New(); Image::Pointer USImage = Image::New(); std::string pathPA = "c:\\ImageData\\" + currentDate + "-" + "PAbeamformed" + ".nrrd"; std::string pathUS = "c:\\ImageData\\" + currentDate + "-" + "USImages" + ".nrrd"; std::string pathTS = "c:\\ImageData\\" + currentDate + "-" + "ts" + ".csv"; std::string pathS = "c:\\ImageData\\" + currentDate + "-" + "Settings" + ".txt"; // idon't forget the raw Images (if chosen to be saved) Image::Pointer PAImageRaw = Image::New(); Image::Pointer USImageRaw = Image::New(); std::string pathPARaw = "c:\\ImageData\\" + currentDate + "-" + "PAraw" + ".nrrd"; std::string pathUSRaw = "c:\\ImageData\\" + currentDate + "-" + "USImagesRaw" + ".nrrd"; if (m_Device->GetScanMode().beamformingAlgorithm == (int)Beamforming::Interleaved_OA_US) // save a PAImage if we used interleaved mode { // first, save the data, so the pyro does not aquire more unneccessary timestamps m_Pyro->SaveData(); // now order the images and save them // the beamformed ones... if (m_SavingSettings.saveBeamformed) { OrderImagesInterleaved(PAImage, USImage, m_RecordedImages, false); mitk::IOUtil::Save(USImage, pathUS); mitk::IOUtil::Save(PAImage, pathPA); } // ...and the raw images if (m_SavingSettings.saveRaw) { OrderImagesInterleaved(PAImageRaw, USImageRaw, m_RawRecordedImages, true); // mitk::IOUtil::Save(USImageRaw, pathUSRaw); mitk::IOUtil::Save(PAImageRaw, pathPARaw); } // read the pixelvalues of the enveloped images at this position itk::Index<3> pixel = { { (itk::Index<3>::IndexValueType)(m_RecordedImages.at(0)->GetDimension(0) / 2), (itk::Index<3>::IndexValueType)(22.0 / 532.0*m_Device->GetScanMode().reconstructionSamplesPerLine), 0 } }; //22/532*2048 = 84 GetPixelValues(pixel, m_PixelValues); // write the Pixelvalues to m_PixelValues // save the timestamps! ofstream timestampFile; timestampFile.open(pathTS); timestampFile << ",timestamp,pixelvalue"; // write the header for (int index = 0; index < m_ImageTimestampRecord.size(); ++index) { timestampFile << "\n" << index << "," << m_ImageTimestampRecord.at(index) << "," << m_PixelValues.at(index); } timestampFile.close(); //save the settings! ofstream settingsFile; settingsFile.open(pathS); auto& sM = m_Device->GetScanMode(); settingsFile << "[General Parameters]\n"; settingsFile << "Scan Depth [mm] = " << sM.receivePhaseLengthSeconds * sM.averageSpeedOfSound / 2 * 1000 << "\n"; settingsFile << "Speed of Sound [m/s] = " << sM.averageSpeedOfSound << "\n"; settingsFile << "Excitation Frequency [MHz] = " << sM.transducerFrequencyHz/1000000 << "\n"; settingsFile << "Voltage [V] = " << sM.voltageV << "\n"; settingsFile << "TGC min = " << (int)sM.tgcdB[0] << " max = " << (int)sM.tgcdB[7] << "\n"; settingsFile << "[Beamforming Parameters]\n"; settingsFile << "Reconstructed Lines = " << sM.reconstructionLines << "\n"; settingsFile << "Samples per Line = " << sM.reconstructionSamplesPerLine << "\n"; settingsFile.close(); } else if (m_Device->GetScanMode().beamformingAlgorithm == (int)Beamforming::PlaneWaveCompound) // save no PAImage if we used US only mode { OrderImagesUltrasound(USImage, m_RecordedImages); mitk::IOUtil::Save(USImage, pathUS); } m_PixelValues.clear(); m_RawRecordedImages.clear(); // clean up the pixel values m_RecordedImages.clear(); // clean up the images m_ImageTimestampRecord.clear(); // clean up the timestamps } } void mitk::USDiPhASImageSource::GetPixelValues(itk::Index<3> pixel, std::vector& values) { unsigned int events = 2; for (int index = 0; index < m_RecordedImages.size(); index += events) // omit sound images { Image::Pointer image = m_RecordedImages.at(index); image = ApplyBmodeFilter(image); values.push_back(image.GetPointer()->GetPixelValueByIndex(pixel)); } } void mitk::USDiPhASImageSource::OrderImagesInterleaved(Image::Pointer PAImage, Image::Pointer USImage, std::vector recordedList, bool raw) { unsigned int width = 32; unsigned int height = 32; unsigned int events = m_Device->GetScanMode().transmitEventsCount + 1; // the PA event is not included in the transmitEvents, so we add 1 here if (!raw) events = 2; // the beamformed image array contains only the resulting image of multiple events if (raw) { width = recordedList.at(0)->GetDimension(0); height = recordedList.at(0)->GetDimension(1); } else if (m_DataType == DataType::Beamformed_Short) { width = m_Device->GetScanMode().reconstructionLines; height = m_Device->GetScanMode().reconstructionSamplesPerLine; } else if (m_DataType == DataType::Image_uChar) { width = m_Device->GetScanMode().imageWidth; height = m_Device->GetScanMode().imageHeight; } unsigned int dimLaser[] = { (unsigned int)width, (unsigned int)height, (unsigned int)(recordedList.size() / events)}; unsigned int dimSound[] = { (unsigned int)width, (unsigned int)height, (unsigned int)(recordedList.size() / events * (events-1))}; PAImage->Initialize(recordedList.back()->GetPixelType(), 3, dimLaser); PAImage->SetGeometry(recordedList.back()->GetGeometry()); USImage->Initialize(recordedList.back()->GetPixelType(), 3, dimSound); USImage->SetGeometry(recordedList.back()->GetGeometry()); for (int index = 0; index < recordedList.size(); ++index) { mitk::ImageReadAccessor inputReadAccessor(recordedList.at(index)); if (index % events == 0) { PAImage->SetSlice(inputReadAccessor.GetData(), index / events); } else { if(!raw) USImage->SetSlice(inputReadAccessor.GetData(), ((index - (index % events)) / events) + (index % events)-1); } } } void mitk::USDiPhASImageSource::OrderImagesUltrasound(Image::Pointer USImage, std::vector recordedList) { unsigned int width = 32; unsigned int height = 32; unsigned int events = m_Device->GetScanMode().transmitEventsCount; if (m_DataType == DataType::Beamformed_Short) { width = (unsigned int)m_Device->GetScanMode().reconstructionLines; height = (unsigned int)m_Device->GetScanMode().reconstructionSamplesPerLine; } else if (m_DataType == DataType::Image_uChar) { width = (unsigned int)m_Device->GetScanMode().imageWidth; height = (unsigned int)m_Device->GetScanMode().imageHeight; } unsigned int dimSound[] = { (unsigned int)width, (unsigned int)height, (unsigned int)recordedList.size()}; USImage->Initialize(recordedList.back()->GetPixelType(), 3, dimSound); USImage->SetGeometry(recordedList.back()->GetGeometry()); for (int index = 0; index < recordedList.size(); ++index) { mitk::ImageReadAccessor inputReadAccessor(recordedList.at(index)); USImage->SetSlice(inputReadAccessor.GetData(), index); } } \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/src/QmitkPAUSViewerView.cpp b/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/src/QmitkPAUSViewerView.cpp index 213a25e502..7fd7f0345e 100644 --- a/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/src/QmitkPAUSViewerView.cpp +++ b/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/src/QmitkPAUSViewerView.cpp @@ -1,159 +1,208 @@ /*=================================================================== 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 #include "mitkScaleLegendAnnotation.h" #include "mitkLayoutAnnotationRenderer.h" #include "mitkManualPlacementAnnotationRenderer.h" #include "mitkTextAnnotation2D.h" #include "QmitkPAUSViewerView.h" +#include +#include + const std::string QmitkPAUSViewerView::VIEW_ID = "org.mitk.views.photoacoustics.pausviewer"; -QmitkPAUSViewerView::QmitkPAUSViewerView() : m_PADataStorage(mitk::StandaloneDataStorage::New()), m_USDataStorage(mitk::StandaloneDataStorage::New()), m_UltrasoundReference(nullptr) +QmitkPAUSViewerView::QmitkPAUSViewerView() : m_PADataStorage(mitk::StandaloneDataStorage::New()), m_USDataStorage(mitk::StandaloneDataStorage::New()) { } QmitkPAUSViewerView::~QmitkPAUSViewerView() { - if(m_UltrasoundReference != nullptr) - *m_UltrasoundReference = nullptr; + this->GetDataStorage()->AddNodeEvent.RemoveListener(mitk::MessageDelegate1(this, &QmitkPAUSViewerView::ScanDataStorage)); + this->GetDataStorage()->AddNodeEvent.RemoveListener(mitk::MessageDelegate1(this, &QmitkPAUSViewerView::RemovedNodeFromStorage)); + this->GetDataStorage()->ChangedNodeEvent.RemoveListener(mitk::MessageDelegate1(this, &QmitkPAUSViewerView::ScanDataStorage)); } void QmitkPAUSViewerView::InitWindows() { AddOverlays(); } void QmitkPAUSViewerView::SetFocus() { } void QmitkPAUSViewerView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*source*/, const QList& /*nodes*/) { } void QmitkPAUSViewerView::CreateQtPartControl(QWidget *parent) { + MITK_INFO << "in here"; m_Controls = new Ui::QmitkPAUSViewerViewControls; m_Controls->setupUi(parent); - m_Controls->m_PARenderWindow->GetRenderer()->SetDataStorage(m_PADataStorage); - m_Controls->m_USRenderWindow->GetRenderer()->SetDataStorage(m_USDataStorage); + SetPADataStorage(m_PADataStorage); + SetUSDataStorage(m_USDataStorage); + + //create a dummy image (gray values 0..255) for correct initialization of level window, etc. + mitk::Image::Pointer dummyImage = mitk::ImageGenerator::GenerateRandomImage(100, 100, 1, 1, 1, 1, 1, 255, 0); + + m_USData = mitk::DataNode::New(); + std::stringstream USnodeName; + USnodeName << "US Image Stream"; + m_USData->SetName(USnodeName.str()); + m_USData->SetData(dummyImage); + m_USDataStorage->Add(m_USData); + + m_PAData = mitk::DataNode::New(); + std::stringstream PAnodeName; + PAnodeName << "PA Image Stream"; + m_PAData->SetName(PAnodeName.str()); + m_PAData->SetData(dummyImage); + m_PADataStorage->Add(m_PAData); + + InitWindows(); + + this->GetDataStorage()->AddNodeEvent.AddListener(mitk::MessageDelegate1(this, &QmitkPAUSViewerView::ScanDataStorage)); + this->GetDataStorage()->RemoveNodeEvent.AddListener(mitk::MessageDelegate1(this, &QmitkPAUSViewerView::RemovedNodeFromStorage)); + this->GetDataStorage()->ChangedNodeEvent.AddListener(mitk::MessageDelegate1(this, &QmitkPAUSViewerView::ScanDataStorage)); + + ScanDataStorage(nullptr); } void QmitkPAUSViewerView::SetPADataStorage(mitk::StandaloneDataStorage::Pointer paStore) { if (m_Controls == nullptr) return; m_PADataStorage = paStore; m_Controls->m_PARenderWindow->GetRenderer()->SetDataStorage(m_PADataStorage); m_Controls->m_PALevelWindow->SetDataStorage(m_PADataStorage); } void QmitkPAUSViewerView::SetUSDataStorage(mitk::StandaloneDataStorage::Pointer usStore) { if (m_Controls == nullptr) return; m_USDataStorage = usStore; m_Controls->m_USRenderWindow->GetRenderer()->SetDataStorage(m_USDataStorage); m_Controls->m_USLevelWindow->SetDataStorage(m_USDataStorage); } vtkRenderWindow* QmitkPAUSViewerView::GetPARenderWindow() { if (m_Controls == nullptr) return nullptr; return m_Controls->m_PARenderWindow->GetRenderWindow(); } vtkRenderWindow* QmitkPAUSViewerView::GetUSRenderWindow() { if (m_Controls == nullptr) return nullptr; return m_Controls->m_USRenderWindow->GetRenderWindow(); } void QmitkPAUSViewerView::AddOverlays() { //if (m_PARenderer == nullptr || /*m_PAOverlayController == nullptr||*/ m_USRenderer == nullptr /*|| m_USOverlayController == nullptr*/) //{ - m_PARenderer = mitk::BaseRenderer::GetInstance(GetPARenderWindow()); - m_USRenderer = mitk::BaseRenderer::GetInstance(GetUSRenderWindow()); + m_PARenderer = mitk::BaseRenderer::GetInstance(GetPARenderWindow()); + m_USRenderer = mitk::BaseRenderer::GetInstance(GetUSRenderWindow()); //} - MITK_INFO << "1111111111111111111111"; mitk::ScaleLegendAnnotation::Pointer scaleAnnotation = mitk::ScaleLegendAnnotation::New(); //scaleAnnotation->SetLeftAxisVisibility(true); //scaleAnnotation->SetRightAxisVisibility(false); //scaleAnnotation->SetRightAxisVisibility(false); //scaleAnnotation->SetTopAxisVisibility(false); //scaleAnnotation->SetCornerOffsetFactor(0); - MITK_INFO << "1111111111111111111111"; // Add Overlays //![TextAnnotation2D] // Create a textAnnotation2D mitk::TextAnnotation2D::Pointer textAnnotation = mitk::TextAnnotation2D::New(); textAnnotation->SetText("Test!"); // set UTF-8 encoded text to render textAnnotation->SetFontSize(40); textAnnotation->SetColor(1, 0, 0); // Set text color to red textAnnotation->SetOpacity(0.5); - MITK_INFO << "1111111111111111111111"; // The position of the Annotation can be set to a fixed coordinate on the display. mitk::Point2D pos; pos[0] = 10; pos[1] = 20; textAnnotation->SetPosition2D(pos); - MITK_INFO << "1111111111111111111111"; std::string rendererID = m_PARenderer->GetName(); // The LayoutAnnotationRenderer can place the TextAnnotation2D at some defined corner positions mitk::LayoutAnnotationRenderer::AddAnnotation( textAnnotation, rendererID, mitk::LayoutAnnotationRenderer::TopLeft, 5, 5, 1); mitk::LayoutAnnotationRenderer::AddAnnotation( textAnnotation, m_PARenderer.GetPointer(), mitk::LayoutAnnotationRenderer::TopLeft, 5, 5, 1); mitk::ManualPlacementAnnotationRenderer::AddAnnotation( textAnnotation, m_PARenderer.GetPointer()); - MITK_INFO << "1111111111111111111111"; mitk::LayoutAnnotationRenderer::AddAnnotation(scaleAnnotation.GetPointer(), m_PARenderer->GetName(), mitk::LayoutAnnotationRenderer::TopLeft, 5, 5, 1); mitk::LayoutAnnotationRenderer::AddAnnotation(scaleAnnotation.GetPointer(), m_USRenderer, mitk::LayoutAnnotationRenderer::TopLeft, 5, 5, 1); - MITK_INFO << "1111111111111111111111"; - } void QmitkPAUSViewerView::RemoveOverlays() { - // m_PAOverlayManager->RemoveAllOverlays(); + // m_PAOverlayManager->RemoveAllOverlays(); } -void QmitkPAUSViewerView::SetUltrasoundReference(QmitkPAUSViewerView** ultrasoundReference) +void QmitkPAUSViewerView::ScanDataStorage(const mitk::DataNode* dataNode) { - m_UltrasoundReference = ultrasoundReference; + auto storage = this->GetDataStorage(); + auto nodeUS = storage->GetNamedNode("US Viewing Stream - Image 0"); + auto nodePA = storage->GetNamedNode("US Viewing Stream - Image 1"); + + if (nodeUS != nullptr) + { + m_USData->SetData(dynamic_cast(nodeUS->GetData())); + } + if (nodePA != nullptr) + { + m_PAData->SetData(dynamic_cast(nodePA->GetData())); + } + auto renderingManager = mitk::RenderingManager::GetInstance(); + renderingManager->RequestUpdate(GetPARenderWindow()); + renderingManager->RequestUpdate(GetUSRenderWindow()); } + +void QmitkPAUSViewerView::RemovedNodeFromStorage(const mitk::DataNode* dataNode) +{ + auto nodeUS = m_USDataStorage->GetNamedNode(dataNode->GetName()); + auto nodePA = m_PADataStorage->GetNamedNode(dataNode->GetName()); + + //create a dummy image (gray values 0..255) for correct initialization of level window, etc. + mitk::Image::Pointer dummyImage = mitk::ImageGenerator::GenerateRandomImage(100, 100, 1, 1, 1, 1, 1, 255, 0); + + m_USData->SetData(dummyImage); + m_PAData->SetData(dummyImage); +} \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/src/QmitkPAUSViewerView.h b/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/src/QmitkPAUSViewerView.h index f9c4d43a96..097ab998bc 100644 --- a/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/src/QmitkPAUSViewerView.h +++ b/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/src/QmitkPAUSViewerView.h @@ -1,74 +1,76 @@ /*=================================================================== 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 QMITKPAUSVIEWERVIEW_H_INCLUDED #define QMITKPAUSVIEWERVIEW_H_INCLUDED #include #include #include #include #include "QmitkRenderWindow.h" #include "ui_QmitkPAUSViewerViewControls.h" #include "org_mitk_gui_qt_photoacoustics_pausviewer_Export.h" #include "mitkCommon.h" class PHOTOACOUSTICS_PAUSVIEWER_EXPORTS QmitkPAUSViewerView : 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; QmitkPAUSViewerView(); virtual ~QmitkPAUSViewerView(); virtual void CreateQtPartControl(QWidget *parent) override; void InitWindows(); void SetPADataStorage(mitk::StandaloneDataStorage::Pointer paStore); void SetUSDataStorage(mitk::StandaloneDataStorage::Pointer usStore); - vtkRenderWindow* GetPARenderWindow(); - vtkRenderWindow* GetUSRenderWindow(); - - void SetUltrasoundReference(QmitkPAUSViewerView** ultrasoundReference); - protected: void AddOverlays(); void RemoveOverlays(); mitk::StandaloneDataStorage::Pointer m_PADataStorage; mitk::StandaloneDataStorage::Pointer m_USDataStorage; + mitk::DataNode::Pointer m_PAData; + mitk::DataNode::Pointer m_USData; mitk::BaseRenderer::Pointer m_PARenderer; mitk::BaseRenderer::Pointer m_USRenderer; virtual void SetFocus() override; virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer, const QList&) override; Ui::QmitkPAUSViewerViewControls* m_Controls; - QmitkPAUSViewerView** m_UltrasoundReference; + + void ScanDataStorage(const mitk::DataNode* dataNode); + void RemovedNodeFromStorage(const mitk::DataNode* dataNode); + + vtkRenderWindow* GetPARenderWindow(); + vtkRenderWindow* GetUSRenderWindow(); }; #endif // QMITKPAUSVIEWERVIEW_H_INCLUDED