diff --git a/Modules/Core/src/IO/mitkItkImageIO.cpp b/Modules/Core/src/IO/mitkItkImageIO.cpp index f0f9a17054..04189f60ee 100644 --- a/Modules/Core/src/IO/mitkItkImageIO.cpp +++ b/Modules/Core/src/IO/mitkItkImageIO.cpp @@ -1,703 +1,703 @@ /*=================================================================== 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 "mitkItkImageIO.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include namespace mitk { const char *const PROPERTY_NAME_TIMEGEOMETRY_TYPE = "org.mitk.timegeometry.type"; const char *const PROPERTY_NAME_TIMEGEOMETRY_TIMEPOINTS = "org.mitk.timegeometry.timepoints"; const char *const PROPERTY_KEY_TIMEGEOMETRY_TYPE = "org_mitk_timegeometry_type"; const char *const PROPERTY_KEY_TIMEGEOMETRY_TIMEPOINTS = "org_mitk_timegeometry_timepoints"; ItkImageIO::ItkImageIO(const ItkImageIO &other) : AbstractFileIO(other), m_ImageIO(dynamic_cast(other.m_ImageIO->Clone().GetPointer())) { this->InitializeDefaultMetaDataKeys(); } std::vector ItkImageIO::FixUpImageIOExtensions(const std::string &imageIOName) { std::vector extensions; // Try to fix-up some known ITK image IO classes if (imageIOName == "GiplImageIO") { extensions.push_back("gipl"); extensions.push_back("gipl.gz"); } else if (imageIOName == "GDCMImageIO") { extensions.push_back("gdcm"); extensions.push_back("dcm"); extensions.push_back("DCM"); extensions.push_back("dc3"); extensions.push_back("DC3"); extensions.push_back("ima"); extensions.push_back("img"); } else if (imageIOName == "PNGImageIO") { extensions.push_back("png"); extensions.push_back("PNG"); } else if (imageIOName == "StimulateImageIO") { extensions.push_back("spr"); } else if (imageIOName == "HDF5ImageIO") { extensions.push_back("hdf"); extensions.push_back("h4"); extensions.push_back("hdf4"); extensions.push_back("h5"); extensions.push_back("hdf5"); extensions.push_back("he4"); extensions.push_back("he5"); extensions.push_back("hd5"); } else if ("GE4ImageIO" == imageIOName || "GE5ImageIO" == imageIOName || "Bruker2dseqImageIO" == imageIOName) { extensions.push_back(""); } if (!extensions.empty()) { MITK_DEBUG << "Fixing up known extensions for " << imageIOName; } return extensions; } void ItkImageIO::FixUpCustomMimeTypeName(const std::string &imageIOName, CustomMimeType &customMimeType) { if ("GE4ImageIO" == imageIOName) { customMimeType.SetName(this->AbstractFileReader::GetMimeTypePrefix() + "ge4"); } else if ("GE5ImageIO" == imageIOName) { customMimeType.SetName(this->AbstractFileReader::GetMimeTypePrefix() + "ge5"); } else if ("Bruker2dseqImageIO" == imageIOName) { customMimeType.SetName(this->AbstractFileReader::GetMimeTypePrefix() + "bruker2dseq"); } } ItkImageIO::ItkImageIO(itk::ImageIOBase::Pointer imageIO) : AbstractFileIO(Image::GetStaticNameOfClass()), m_ImageIO(imageIO) { if (m_ImageIO.IsNull()) { mitkThrow() << "ITK ImageIOBase argument must not be nullptr"; } this->AbstractFileReader::SetMimeTypePrefix(IOMimeTypes::DEFAULT_BASE_NAME() + ".image."); this->InitializeDefaultMetaDataKeys(); std::vector readExtensions = m_ImageIO->GetSupportedReadExtensions(); if (readExtensions.empty()) { std::string imageIOName = m_ImageIO->GetNameOfClass(); MITK_DEBUG << "ITK ImageIOBase " << imageIOName << " does not provide read extensions"; readExtensions = FixUpImageIOExtensions(imageIOName); } CustomMimeType customReaderMimeType; customReaderMimeType.SetCategory("Images"); for (std::vector::const_iterator iter = readExtensions.begin(), endIter = readExtensions.end(); iter != endIter; ++iter) { std::string extension = *iter; if (!extension.empty() && extension[0] == '.') { extension.assign(iter->begin() + 1, iter->end()); } customReaderMimeType.AddExtension(extension); } auto extensions = customReaderMimeType.GetExtensions(); if (extensions.empty() || (extensions.size() == 1 && extensions[0].empty())) { std::string imageIOName = m_ImageIO->GetNameOfClass(); FixUpCustomMimeTypeName(imageIOName, customReaderMimeType); } this->AbstractFileReader::SetMimeType(customReaderMimeType); std::vector writeExtensions = imageIO->GetSupportedWriteExtensions(); if (writeExtensions.empty()) { std::string imageIOName = imageIO->GetNameOfClass(); MITK_DEBUG << "ITK ImageIOBase " << imageIOName << " does not provide write extensions"; writeExtensions = FixUpImageIOExtensions(imageIOName); } if (writeExtensions != readExtensions) { CustomMimeType customWriterMimeType; customWriterMimeType.SetCategory("Images"); for (std::vector::const_iterator iter = writeExtensions.begin(), endIter = writeExtensions.end(); iter != endIter; ++iter) { std::string extension = *iter; if (!extension.empty() && extension[0] == '.') { extension.assign(iter->begin() + 1, iter->end()); } customWriterMimeType.AddExtension(extension); } auto extensions = customWriterMimeType.GetExtensions(); if (extensions.empty() || (extensions.size() == 1 && extensions[0].empty())) { std::string imageIOName = m_ImageIO->GetNameOfClass(); FixUpCustomMimeTypeName(imageIOName, customWriterMimeType); } this->AbstractFileWriter::SetMimeType(customWriterMimeType); } std::string description = std::string("ITK ") + imageIO->GetNameOfClass(); this->SetReaderDescription(description); this->SetWriterDescription(description); this->RegisterService(); } ItkImageIO::ItkImageIO(const CustomMimeType &mimeType, itk::ImageIOBase::Pointer imageIO, int rank) : AbstractFileIO(Image::GetStaticNameOfClass(), mimeType, std::string("ITK ") + imageIO->GetNameOfClass()), m_ImageIO(imageIO) { if (m_ImageIO.IsNull()) { mitkThrow() << "ITK ImageIOBase argument must not be nullptr"; } this->AbstractFileReader::SetMimeTypePrefix(IOMimeTypes::DEFAULT_BASE_NAME() + ".image."); this->InitializeDefaultMetaDataKeys(); if (rank) { this->AbstractFileReader::SetRanking(rank); this->AbstractFileWriter::SetRanking(rank); } this->RegisterService(); } /**Helper function that converts the content of a meta data into a time point vector. * If MetaData is not valid or cannot be converted an empty vector is returned.*/ std::vector ConvertMetaDataObjectToTimePointList(const itk::MetaDataObjectBase *data) { const auto *timeGeometryTimeData = dynamic_cast *>(data); std::vector result; if (timeGeometryTimeData) { std::string dataStr = timeGeometryTimeData->GetMetaDataObjectValue(); std::stringstream stream(dataStr); TimePointType tp; while (stream >> tp) { result.push_back(tp); } } return result; }; std::vector ItkImageIO::Read() { std::vector result; mitk::LocaleSwitch localeSwitch("C"); Image::Pointer image = Image::New(); const unsigned int MINDIM = 2; const unsigned int MAXDIM = 4; const std::string path = this->GetLocalFileName(); MITK_INFO << "loading " << path << " via itk::ImageIOFactory... " << std::endl; // Check to see if we can read the file given the name or prefix if (path.empty()) { mitkThrow() << "Empty filename in mitk::ItkImageIO "; } // Got to allocate space for the image. Determine the characteristics of // the image. m_ImageIO->SetFileName(path); m_ImageIO->ReadImageInformation(); unsigned int ndim = m_ImageIO->GetNumberOfDimensions(); if (ndim < MINDIM || ndim > MAXDIM) { MITK_WARN << "Sorry, only dimensions 2, 3 and 4 are supported. The given file has " << ndim << " dimensions! Reading as 4D."; ndim = MAXDIM; } itk::ImageIORegion ioRegion(ndim); itk::ImageIORegion::SizeType ioSize = ioRegion.GetSize(); itk::ImageIORegion::IndexType ioStart = ioRegion.GetIndex(); unsigned int dimensions[MAXDIM]; dimensions[0] = 0; dimensions[1] = 0; dimensions[2] = 0; dimensions[3] = 0; ScalarType spacing[MAXDIM]; spacing[0] = 1.0f; spacing[1] = 1.0f; spacing[2] = 1.0f; spacing[3] = 1.0f; Point3D origin; origin.Fill(0); unsigned int i; for (i = 0; i < ndim; ++i) { ioStart[i] = 0; ioSize[i] = m_ImageIO->GetDimensions(i); if (i < MAXDIM) { dimensions[i] = m_ImageIO->GetDimensions(i); spacing[i] = m_ImageIO->GetSpacing(i); if (spacing[i] <= 0) spacing[i] = 1.0f; } if (i < 3) { origin[i] = m_ImageIO->GetOrigin(i); } } ioRegion.SetSize(ioSize); ioRegion.SetIndex(ioStart); MITK_INFO << "ioRegion: " << ioRegion << std::endl; m_ImageIO->SetIORegion(ioRegion); void *buffer = new unsigned char[m_ImageIO->GetImageSizeInBytes()]; m_ImageIO->Read(buffer); image->Initialize(MakePixelType(m_ImageIO), ndim, dimensions); image->SetImportChannel(buffer, 0, Image::ManageMemory); const itk::MetaDataDictionary &dictionary = m_ImageIO->GetMetaDataDictionary(); // access direction of itk::Image and include spacing mitk::Matrix3D matrix; matrix.SetIdentity(); unsigned int j, itkDimMax3 = (ndim >= 3 ? 3 : ndim); for (i = 0; i < itkDimMax3; ++i) for (j = 0; j < itkDimMax3; ++j) matrix[i][j] = m_ImageIO->GetDirection(j)[i]; // re-initialize PlaneGeometry with origin and direction PlaneGeometry *planeGeometry = image->GetSlicedGeometry(0)->GetPlaneGeometry(0); planeGeometry->SetOrigin(origin); planeGeometry->GetIndexToWorldTransform()->SetMatrix(matrix); // re-initialize SlicedGeometry3D SlicedGeometry3D *slicedGeometry = image->GetSlicedGeometry(0); slicedGeometry->InitializeEvenlySpaced(planeGeometry, image->GetDimension(2)); slicedGeometry->SetSpacing(spacing); MITK_INFO << slicedGeometry->GetCornerPoint(false, false, false); MITK_INFO << slicedGeometry->GetCornerPoint(true, true, true); // re-initialize TimeGeometry TimeGeometry::Pointer timeGeometry; if (dictionary.HasKey(PROPERTY_NAME_TIMEGEOMETRY_TYPE) || dictionary.HasKey(PROPERTY_KEY_TIMEGEOMETRY_TYPE)) { // also check for the name because of backwards compatibility. Past code version stored with the name and not with // the key itk::MetaDataObject::ConstPointer timeGeometryTypeData = nullptr; if (dictionary.HasKey(PROPERTY_NAME_TIMEGEOMETRY_TYPE)) { timeGeometryTypeData = dynamic_cast *>(dictionary.Get(PROPERTY_NAME_TIMEGEOMETRY_TYPE)); } else { timeGeometryTypeData = dynamic_cast *>(dictionary.Get(PROPERTY_KEY_TIMEGEOMETRY_TYPE)); } if (timeGeometryTypeData->GetMetaDataObjectValue() == ArbitraryTimeGeometry::GetStaticNameOfClass()) { MITK_INFO << "used time geometry: " << ArbitraryTimeGeometry::GetStaticNameOfClass() << std::endl; typedef std::vector TimePointVector; TimePointVector timePoints; if (dictionary.HasKey(PROPERTY_NAME_TIMEGEOMETRY_TIMEPOINTS)) { timePoints = ConvertMetaDataObjectToTimePointList(dictionary.Get(PROPERTY_NAME_TIMEGEOMETRY_TIMEPOINTS)); } else if (dictionary.HasKey(PROPERTY_KEY_TIMEGEOMETRY_TIMEPOINTS)) { timePoints = ConvertMetaDataObjectToTimePointList(dictionary.Get(PROPERTY_KEY_TIMEGEOMETRY_TIMEPOINTS)); } if (timePoints.size() - 1 != image->GetDimension(3)) { MITK_ERROR << "Stored timepoints (" << timePoints.size() - 1 << ") and size of image time dimension (" << image->GetDimension(3) << ") do not match. Switch to ProportionalTimeGeometry fallback" << std::endl; } else { ArbitraryTimeGeometry::Pointer arbitraryTimeGeometry = ArbitraryTimeGeometry::New(); TimePointVector::const_iterator pos = timePoints.begin(); auto prePos = pos++; for (; pos != timePoints.end(); ++prePos, ++pos) { arbitraryTimeGeometry->AppendNewTimeStepClone(slicedGeometry, *prePos, *pos); } timeGeometry = arbitraryTimeGeometry; } } } if (timeGeometry.IsNull()) { // Fallback. If no other valid time geometry has been created, create a ProportionalTimeGeometry MITK_INFO << "used time geometry: " << ProportionalTimeGeometry::GetStaticNameOfClass() << std::endl; ProportionalTimeGeometry::Pointer propTimeGeometry = ProportionalTimeGeometry::New(); propTimeGeometry->Initialize(slicedGeometry, image->GetDimension(3)); timeGeometry = propTimeGeometry; } image->SetTimeGeometry(timeGeometry); buffer = nullptr; MITK_INFO << "number of image components: " << image->GetPixelType().GetNumberOfComponents() << std::endl; for (auto iter = dictionary.Begin(), iterEnd = dictionary.End(); iter != iterEnd; ++iter) { if (iter->second->GetMetaDataObjectTypeInfo() == typeid(std::string)) { const std::string &key = iter->first; std::string assumedPropertyName = key; std::replace(assumedPropertyName.begin(), assumedPropertyName.end(), '_', '.'); std::string mimeTypeName = GetMimeType()->GetName(); // Check if there is already a info for the key and our mime type. IPropertyPersistence::InfoResultType infoList = mitk::CoreServices::GetPropertyPersistence()->GetInfoByKey(key); auto predicate = [mimeTypeName](const PropertyPersistenceInfo::ConstPointer &x) { return x.IsNotNull() && x->GetMimeTypeName() == mimeTypeName; }; auto finding = std::find_if(infoList.begin(), infoList.end(), predicate); if (finding == infoList.end()) { auto predicateWild = [](const PropertyPersistenceInfo::ConstPointer &x) { return x.IsNotNull() && x->GetMimeTypeName() == PropertyPersistenceInfo::ANY_MIMETYPE_NAME(); }; finding = std::find_if(infoList.begin(), infoList.end(), predicateWild); } PropertyPersistenceInfo::ConstPointer info; if (finding != infoList.end()) { assumedPropertyName = (*finding)->GetName(); info = *finding; } else { // we have not found anything suitable so we generate our own info PropertyPersistenceInfo::Pointer newInfo = PropertyPersistenceInfo::New(); newInfo->SetNameAndKey(assumedPropertyName, key); newInfo->SetMimeTypeName(PropertyPersistenceInfo::ANY_MIMETYPE_NAME()); info = newInfo; } std::string value = dynamic_cast *>(iter->second.GetPointer())->GetMetaDataObjectValue(); mitk::BaseProperty::Pointer loadedProp = info->GetDeserializationFunction()(value); image->SetProperty(assumedPropertyName.c_str(), loadedProp); // Read properties should be persisted unless they are default properties // which are written anyway bool isDefaultKey(false); for (const auto &defaultKey : m_DefaultMetaDataKeys) { if (defaultKey.length() <= assumedPropertyName.length()) { // does the start match the default key if (assumedPropertyName.substr(0, defaultKey.length()).find(defaultKey) != std::string::npos) { isDefaultKey = true; break; } } } if (!isDefaultKey) { mitk::CoreServices::GetPropertyPersistence()->AddInfo(info); } } } MITK_INFO << "...finished!" << std::endl; result.push_back(image.GetPointer()); return result; } AbstractFileIO::ConfidenceLevel ItkImageIO::GetReaderConfidenceLevel() const { return m_ImageIO->CanReadFile(GetLocalFileName().c_str()) ? IFileReader::Supported : IFileReader::Unsupported; } void ItkImageIO::Write() { const auto *image = dynamic_cast(this->GetInput()); if (image == nullptr) { mitkThrow() << "Cannot write non-image data"; } // Switch the current locale to "C" LocaleSwitch localeSwitch("C"); // Clone the image geometry, because we might have to change it // for writing purposes BaseGeometry::Pointer geometry = image->GetGeometry()->Clone(); // Check if geometry information will be lost if (image->GetDimension() == 2 && !geometry->Is2DConvertable()) { MITK_WARN << "Saving a 2D image with 3D geometry information. Geometry information will be lost! You might " "consider using Convert2Dto3DImageFilter before saving."; // set matrix to identity mitk::AffineTransform3D::Pointer affTrans = mitk::AffineTransform3D::New(); affTrans->SetIdentity(); mitk::Vector3D spacing = geometry->GetSpacing(); mitk::Point3D origin = geometry->GetOrigin(); geometry->SetIndexToWorldTransform(affTrans); geometry->SetSpacing(spacing); geometry->SetOrigin(origin); } LocalFile localFile(this); const std::string path = localFile.GetFileName(); MITK_INFO << "Writing image: " << path << std::endl; try { // Implementation of writer using itkImageIO directly. This skips the use // of templated itkImageFileWriter, which saves the multiplexing on MITK side. const unsigned int dimension = image->GetDimension(); const unsigned int *const dimensions = image->GetDimensions(); const mitk::PixelType pixelType = image->GetPixelType(); const mitk::Vector3D mitkSpacing = geometry->GetSpacing(); const mitk::Point3D mitkOrigin = geometry->GetOrigin(); // Due to templating in itk, we are forced to save a 4D spacing and 4D Origin, // though they are not supported in MITK itk::Vector spacing4D; spacing4D[0] = mitkSpacing[0]; spacing4D[1] = mitkSpacing[1]; spacing4D[2] = mitkSpacing[2]; spacing4D[3] = 1; // There is no support for a 4D spacing. However, we should have a valid value here itk::Vector origin4D; origin4D[0] = mitkOrigin[0]; origin4D[1] = mitkOrigin[1]; origin4D[2] = mitkOrigin[2]; origin4D[3] = 0; // There is no support for a 4D origin. However, we should have a valid value here // Set the necessary information for imageIO m_ImageIO->SetNumberOfDimensions(dimension); m_ImageIO->SetPixelType(pixelType.GetPixelType()); m_ImageIO->SetComponentType(pixelType.GetComponentType() < PixelComponentUserType ? static_cast(pixelType.GetComponentType()) : itk::ImageIOBase::UNKNOWNCOMPONENTTYPE); m_ImageIO->SetNumberOfComponents(pixelType.GetNumberOfComponents()); itk::ImageIORegion ioRegion(dimension); for (unsigned int i = 0; i < dimension; i++) { m_ImageIO->SetDimensions(i, dimensions[i]); m_ImageIO->SetSpacing(i, spacing4D[i]); m_ImageIO->SetOrigin(i, origin4D[i]); mitk::Vector3D mitkDirection; mitkDirection.SetVnlVector(geometry->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(i)); itk::Vector direction4D; direction4D[0] = mitkDirection[0]; direction4D[1] = mitkDirection[1]; direction4D[2] = mitkDirection[2]; // MITK only supports a 3x3 direction matrix. Due to templating in itk, however, we must // save a 4x4 matrix for 4D images. in this case, add an homogneous component to the matrix. if (i == 3) { direction4D[3] = 1; // homogenous component } else { direction4D[3] = 0; } vnl_vector axisDirection(dimension); for (unsigned int j = 0; j < dimension; j++) { axisDirection[j] = direction4D[j] / spacing4D[i]; } m_ImageIO->SetDirection(i, axisDirection); ioRegion.SetSize(i, image->GetLargestPossibleRegion().GetSize(i)); ioRegion.SetIndex(i, image->GetLargestPossibleRegion().GetIndex(i)); } // use compression if available - m_ImageIO->UseCompressionOn(); + //m_ImageIO->UseCompressionOn(); m_ImageIO->SetIORegion(ioRegion); m_ImageIO->SetFileName(path); // Handle time geometry const auto *arbitraryTG = dynamic_cast(image->GetTimeGeometry()); if (arbitraryTG) { itk::EncapsulateMetaData(m_ImageIO->GetMetaDataDictionary(), PROPERTY_KEY_TIMEGEOMETRY_TYPE, ArbitraryTimeGeometry::GetStaticNameOfClass()); std::stringstream stream; stream << arbitraryTG->GetTimeBounds(0)[0]; for (TimeStepType pos = 0; pos < arbitraryTG->CountTimeSteps(); ++pos) { stream << " " << arbitraryTG->GetTimeBounds(pos)[1]; } std::string data = stream.str(); itk::EncapsulateMetaData( m_ImageIO->GetMetaDataDictionary(), PROPERTY_KEY_TIMEGEOMETRY_TIMEPOINTS, data); } // Handle properties mitk::PropertyList::Pointer imagePropertyList = image->GetPropertyList(); for (const auto &property : *imagePropertyList->GetMap()) { IPropertyPersistence::InfoResultType infoList = mitk::CoreServices::GetPropertyPersistence()->GetInfo(property.first, GetMimeType()->GetName(), true); if (infoList.empty()) { continue; } std::string value = infoList.front()->GetSerializationFunction()(property.second); if (value == mitk::BaseProperty::VALUE_CANNOT_BE_CONVERTED_TO_STRING) { continue; } std::string key = infoList.front()->GetKey(); itk::EncapsulateMetaData(m_ImageIO->GetMetaDataDictionary(), key, value); } ImageReadAccessor imageAccess(image); LocaleSwitch localeSwitch2("C"); m_ImageIO->Write(imageAccess.GetData()); } catch (const std::exception &e) { mitkThrow() << e.what(); } } AbstractFileIO::ConfidenceLevel ItkImageIO::GetWriterConfidenceLevel() const { // Check if the image dimension is supported const auto *image = dynamic_cast(this->GetInput()); if (image == nullptr) { // We cannot write a null object, DUH! return IFileWriter::Unsupported; } if (!m_ImageIO->SupportsDimension(image->GetDimension())) { // okay, dimension is not supported. We have to look at a special case: // 3D-Image with one slice. We can treat that as a 2D image. if ((image->GetDimension() == 3) && (image->GetSlicedGeometry()->GetSlices() == 1)) return IFileWriter::Supported; else return IFileWriter::Unsupported; } // Check if geometry information will be lost if (image->GetDimension() == 2 && !image->GetGeometry()->Is2DConvertable()) { return IFileWriter::PartiallySupported; } return IFileWriter::Supported; } ItkImageIO *ItkImageIO::IOClone() const { return new ItkImageIO(*this); } void ItkImageIO::InitializeDefaultMetaDataKeys() { this->m_DefaultMetaDataKeys.push_back("NRRD.space"); this->m_DefaultMetaDataKeys.push_back("NRRD.kinds"); this->m_DefaultMetaDataKeys.push_back(PROPERTY_NAME_TIMEGEOMETRY_TYPE); this->m_DefaultMetaDataKeys.push_back(PROPERTY_NAME_TIMEGEOMETRY_TIMEPOINTS); this->m_DefaultMetaDataKeys.push_back("ITK.InputFilterName"); } } diff --git a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASDevice.cpp b/Modules/US/USHardwareDiPhAS/mitkUSDiPhASDevice.cpp index ed9942b062..bdd8d914aa 100644 --- a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASDevice.cpp +++ b/Modules/US/USHardwareDiPhAS/mitkUSDiPhASDevice.cpp @@ -1,308 +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; + m_ScanMode.triggerSetup.delayTrigger2Microseconds = 290; } // 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 e570f4fa73..5b565556d4 100644 --- a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASImageSource.cpp +++ b/Modules/US/USHardwareDiPhAS/mitkUSDiPhASImageSource.cpp @@ -1,1031 +1,1035 @@ /*=================================================================== 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" #include // itk dependencies #include "itkImage.h" #include "itkResampleImageFilter.h" #include "itkCastImageFilter.h" #include "itkCropImageFilter.h" #include "itkRescaleIntensityImageFilter.h" #include "itkIntensityWindowingImageFilter.h" #include #include "itkMultiplyImageFilter.h" mitk::USDiPhASImageSource::USDiPhASImageSource(mitk::USDiPhASDevice* device) : m_Device(device), m_StartTime(((float)std::clock()) / CLOCKS_PER_SEC), m_DataType(DataType::Image_uChar), m_UseBModeFilter(false), m_CurrentlyRecording(false), m_DataTypeModified(true), m_DataTypeNext(DataType::Image_uChar), m_RecordedImageCounter(0), m_PyroConnected(false), 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_BatchSize(24), // why? because magic number, thats why! m_SavingName("-replace"), m_BufferBatches(12), // we like magic numbers m_LastImage(0) { // fill the Recording Buffers with empty images m_ImagesBuffer.insert(m_ImagesBuffer.begin(),m_BufferBatches, std::vector>()); m_RawImagesBuffer.insert(m_RawImagesBuffer.begin(),m_BufferBatches, std::vector>()); m_ImageTimestampsBuffer.insert(m_ImageTimestampsBuffer.begin(),m_BufferBatches, std::vector()); for (int i = 0; i (mitk::Image::New(), mitk::Image::New())); m_RawImagesBuffer[i].insert(m_RawImagesBuffer[i].begin(), m_BatchSize, std::pair(mitk::Image::New(), mitk::Image::New())); m_ImageTimestampsBuffer[i].insert(m_ImageTimestampsBuffer[i].begin(), m_BatchSize, 0); } m_LastBatch = 0; m_LastImage = -1; 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::Load(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::CheckModifiedVariables() { // modify all settings that have been changed here, so we don't get multithreading issues if (m_DataTypeModified) { SetDataType(m_DataTypeNext); m_DataTypeModified = false; UpdateImageGeometry(); } if (m_UseBModeFilterModified) { SetUseBModeFilter(m_UseBModeFilterNext); m_UseBModeFilterModified = false; } if (m_VerticalSpacingModified) { m_VerticalSpacing = m_VerticalSpacingNext; m_VerticalSpacingModified = false; } if (m_ScatteringCoefficientModified) { m_ScatteringCoefficient = m_ScatteringCoefficientNext; m_ScatteringCoefficientModified = false; } if (m_CompensateForScatteringModified) { m_CompensateForScattering = m_CompensateForScatteringNext; m_CompensateForScatteringModified = false; } if (m_CompensateEnergyModified) { m_CompensateEnergy = m_CompensateEnergyNext; m_CompensateEnergyModified = false; } } void mitk::USDiPhASImageSource::ResizeFluenceImage(mitk::Vector3D spacing, unsigned int* dimensions) { auto curResizeImage = ApplyResampling(m_FluenceCompOriginal.at(m_ScatteringCoefficient), spacing, dimensions); unsigned int imageSize = dimensions[0] * dimensions[1]; double* rawOutputData = new double[imageSize]; double* rawScatteringData = (double*)curResizeImage->GetData(); unsigned int sizeRawScatteringData = curResizeImage->GetDimension(0) * curResizeImage->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; unsigned int lowerBound = std::round(upperCutoffmm / spacing[1])*dimensions[0]; unsigned int upperBound = lowerBound + sizeRawScatteringData; for (unsigned int i = 0; i < lowerBound && i < imageSize; ++i) { rawOutputData[i] = 0; // everything than cannot be compensated shall be treated as garbage, here the upper 0.15mm } for (unsigned int i = lowerBound; i < upperBound && i < imageSize; ++i) { rawOutputData[i] = 1 / rawScatteringData[i - lowerBound]; } for (unsigned int i = upperBound; i < imageSize; ++i) { rawOutputData[i] = 0; // everything than cannot be compensated shall be treated as garbage } unsigned int dim[] = { dimensions[0], dimensions[1], 1 }; curResizeImage->Initialize(mitk::MakeScalarPixelType(), 3, dim); curResizeImage->SetSpacing(spacing); curResizeImage->SetSlice(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."; delete[] rawOutputData; } void mitk::USDiPhASImageSource::GetNextRawImage(std::vector& imageVector) { CheckModifiedVariables(); if (imageVector.size() != 2) { imageVector.resize(2); } if (m_LastImage == -1) return; // make sure image is nullptr mitk::Image::Pointer imageUS = nullptr; mitk::Image::Pointer imagePA = nullptr; float ImageEnergyValue = 0; imagePA = m_ImagesBuffer[m_LastBatch][m_LastImage].first; imageUS = m_ImagesBuffer[m_LastBatch][m_LastImage].second; ImageEnergyValue = 1; if (imagePA == nullptr || imageUS == nullptr || !imagePA->IsInitialized() || !imageUS->IsInitialized()) return; // do image processing before displaying it if(imagePA.IsNotNull() && m_DataType == DataType::Beamformed_Short) { itkFloatImageType::Pointer itkImage; mitk::CastToItkImage(imagePA, itkImage); imagePA = mitk::GrabItkImageMemory(itkImage); //thereby using float images imagePA = CutOffTop(imagePA, 165); if (m_CompensateEnergy && ImageEnergyValue != 1) imagePA = MultiplyImage(imagePA, 1 / ImageEnergyValue); // TODO: add the correct prefactor here if (m_UseBModeFilter) imagePA = ApplyBmodeFilter(imagePA, false); if (m_VerticalSpacing) imagePA = ResampleOutputVertical(imagePA, m_VerticalSpacing); if (m_CompensateForScattering) { auto curResizeImage = m_FluenceCompResized.at(m_ScatteringCoefficient); bool doResampling = imagePA->GetDimension(0) != curResizeImage->GetDimension(0) || imagePA->GetDimension(1) != curResizeImage->GetDimension(1) || imagePA->GetGeometry()->GetSpacing()[0] != curResizeImage->GetGeometry()->GetSpacing()[0] || imagePA->GetGeometry()->GetSpacing()[1] != curResizeImage->GetGeometry()->GetSpacing()[1]; if (doResampling) ResizeFluenceImage(imagePA->GetGeometry()->GetSpacing(), imagePA->GetDimensions()); imagePA = ApplyScatteringCompensation(imagePA, m_ScatteringCoefficient); } } if(imageUS.IsNotNull() && m_DataType == DataType::Beamformed_Short) { itkFloatImageType::Pointer itkImage; mitk::CastToItkImage(imageUS, itkImage); imageUS = mitk::GrabItkImageMemory(itkImage); //thereby using float images imageUS = CutOffTop(imageUS, 165); if (m_UseBModeFilter) imageUS = ApplyBmodeFilter(imageUS, true); // the US Images get a logarithmic filter if (m_VerticalSpacing) imageUS = ResampleOutputVertical(imageUS, m_VerticalSpacing); } imageVector[0] = imagePA; imageVector[1] = imageUS; } mitk::Image::Pointer mitk::USDiPhASImageSource::ApplyBmodeFilter(mitk::Image::Pointer image, bool useLogFilter) { // we use this seperate ApplyBmodeFilter Method for processing of two-dimensional images // the image needs to be of floating point type for the envelope filter to work; the casting is done automatically by the CastToItkImage typedef itk::BModeImageFilter < itkFloatImageType, itkFloatImageType > BModeFilterType; BModeFilterType::Pointer bModeFilter = BModeFilterType::New(); // LogFilter typedef itk::PhotoacousticBModeImageFilter < itkFloatImageType, itkFloatImageType > PhotoacousticBModeImageFilter; PhotoacousticBModeImageFilter::Pointer photoacousticBModeFilter = PhotoacousticBModeImageFilter::New(); // No LogFilter itkFloatImageType::Pointer itkImage; itkFloatImageType::Pointer bmode; mitk::CastToItkImage(image, itkImage); if (useLogFilter) { bModeFilter->SetInput(itkImage); bModeFilter->SetDirection(1); bmode = bModeFilter->GetOutput(); } else { photoacousticBModeFilter->SetInput(itkImage); photoacousticBModeFilter->SetDirection(1); bmode = photoacousticBModeFilter->GetOutput(); } return mitk::GrabItkImageMemory(bmode); } mitk::Image::Pointer mitk::USDiPhASImageSource::CutOffTop(mitk::Image::Pointer image, int cutOffSize) { typedef itk::CropImageFilter < itkFloatImageType, itkFloatImageType > CutImageFilter; itkFloatImageType::SizeType cropSize; itkFloatImageType::Pointer itkImage; mitk::CastToItkImage(image, itkImage); cropSize[0] = 0; if(itkImage->GetLargestPossibleRegion().GetSize()[1] == 2048) cropSize[1] = cutOffSize; else cropSize[1] = 0; cropSize[2] = 0; CutImageFilter::Pointer cutOffFilter = CutImageFilter::New(); cutOffFilter->SetInput(itkImage); cutOffFilter->SetLowerBoundaryCropSize(cropSize); cutOffFilter->UpdateLargestPossibleRegion(); return mitk::GrabItkImageMemory(cutOffFilter->GetOutput()); } mitk::Image::Pointer mitk::USDiPhASImageSource::ResampleOutputVertical(mitk::Image::Pointer image, float verticalSpacing) { typedef itk::ResampleImageFilter < itkFloatImageType, itkFloatImageType > ResampleImageFilter; ResampleImageFilter::Pointer resampleImageFilter = ResampleImageFilter::New(); itkFloatImageType::Pointer itkImage; mitk::CastToItkImage(image, itkImage); itkFloatImageType::SpacingType outputSpacing; itkFloatImageType::SizeType inputSize = itkImage->GetLargestPossibleRegion().GetSize(); itkFloatImageType::SizeType outputSize = inputSize; outputSpacing[0] = itkImage->GetSpacing()[0] * (static_cast(inputSize[0]) / static_cast(outputSize[0])); outputSpacing[1] = verticalSpacing; outputSpacing[2] = itkImage->GetSpacing()[2]; outputSize[1] = inputSize[1] * itkImage->GetSpacing()[1] / outputSpacing[1]; typedef itk::IdentityTransform TransformType; resampleImageFilter->SetInput(itkImage); resampleImageFilter->SetSize(outputSize); resampleImageFilter->SetOutputSpacing(outputSpacing); resampleImageFilter->SetTransform(TransformType::New()); resampleImageFilter->UpdateLargestPossibleRegion(); return mitk::GrabItkImageMemory(resampleImageFilter->GetOutput()); } mitk::Image::Pointer mitk::USDiPhASImageSource::ApplyScatteringCompensation(mitk::Image::Pointer inputImage, int scattering) { typedef itk::MultiplyImageFilter MultiplyImageFilterType; itkFloatImageType::Pointer itkImage; mitk::CastToItkImage(inputImage, itkImage); MultiplyImageFilterType::Pointer multiplyFilter = MultiplyImageFilterType::New(); multiplyFilter->SetInput1(itkImage); multiplyFilter->SetInput2(m_FluenceCompResizedItk.at(m_ScatteringCoefficient)); return mitk::GrabItkImageMemory(multiplyFilter->GetOutput()); } mitk::Image::Pointer mitk::USDiPhASImageSource::ApplyResampling(mitk::Image::Pointer inputImage, mitk::Vector3D outputSpacing, unsigned int outputSize[3]) { typedef itk::ResampleImageFilter < itkFloatImageType, itkFloatImageType > ResampleImageFilter; ResampleImageFilter::Pointer resampleImageFilter = ResampleImageFilter::New(); itkFloatImageType::Pointer itkImage; mitk::CastToItkImage(inputImage, itkImage); itkFloatImageType::SpacingType outputSpacingItk; itkFloatImageType::SizeType inputSizeItk = itkImage->GetLargestPossibleRegion().GetSize(); itkFloatImageType::SizeType outputSizeItk = inputSizeItk; itkFloatImageType::SpacingType inputSpacing = itkImage->GetSpacing(); outputSizeItk[0] = outputSize[0]; outputSizeItk[1] = 10 * (inputSpacing[1] * inputSizeItk[1]) / (outputSpacing[1]); outputSizeItk[2] = 1; outputSpacingItk[0] = 0.996 * inputSpacing[0] * (static_cast(inputSizeItk[0]) / static_cast(outputSizeItk[0])); // TODO: find out why the spacing is not correct, so we need that factor; ?!?! outputSpacingItk[1] = inputSpacing[1] * (static_cast(inputSizeItk[1]) / static_cast(outputSizeItk[1])); outputSpacingItk[2] = outputSpacing[2]; typedef itk::IdentityTransform TransformType; resampleImageFilter->SetInput(itkImage); resampleImageFilter->SetSize(outputSizeItk); resampleImageFilter->SetOutputSpacing(outputSpacingItk); resampleImageFilter->SetTransform(TransformType::New()); resampleImageFilter->UpdateLargestPossibleRegion(); return mitk::GrabItkImageMemory(resampleImageFilter->GetOutput()); } mitk::Image::Pointer mitk::USDiPhASImageSource::MultiplyImage(mitk::Image::Pointer inputImage, double value) { typedef itk::MultiplyImageFilter MultiplyImageFilterType; itkFloatImageType::Pointer itkImage; mitk::CastToItkImage(inputImage, itkImage); MultiplyImageFilterType::Pointer multiplyFilter = MultiplyImageFilterType::New(); multiplyFilter->SetInput1(itkImage); multiplyFilter->SetConstant(value); return mitk::GrabItkImageMemory(multiplyFilter->GetOutput()); } void mitk::USDiPhASImageSource::ImageDataCallback( short* rfDataChannelData, int& channelDataChannelsPerDataset, int& channelDataSamplesPerChannel, int& channelDataTotalDatasets, short* rfDataArrayBeamformed, int& beamformedLines, int& beamformedSamples, int& beamformedTotalDatasets, unsigned char* imageData, int& imageWidth, int& imageHeight, int& imageBytesPerPixel, int& imageSetsTotal, double& timeStamp) { if (m_DataTypeModified) return; if (!m_PyroConnected) { m_Pyro = mitk::OphirPyro::New(); MITK_INFO << "[Pyro Debug] OpenConnection: " << m_Pyro->OpenConnection(); MITK_INFO << "[Pyro Debug] StartDataAcquisition: " << m_Pyro->StartDataAcquisition(); m_PyroConnected = true; } bool writeImage = ((m_DataType == DataType::Image_uChar) && (imageData != nullptr)) || ((m_DataType == DataType::Beamformed_Short) && (rfDataArrayBeamformed != nullptr)); if (writeImage) { int currentBatch = -1; int currentImage = -1; long long currentImageTimestamp = std::chrono::high_resolution_clock::now().time_since_epoch().count(); // check whether we lost any images if (m_CurrentlyRecording && m_ImageTimestampsBuffer[m_LastBatch][m_LastImage] != 0 && std::abs(currentImageTimestamp - m_ImageTimestampsBuffer[m_LastBatch][m_LastImage]) > 53 * std::pow(10, 6)) { MITK_ERROR << "Lost about " << (float)std::abs(currentImageTimestamp - m_ImageTimestampsBuffer[m_LastBatch][m_LastImage]) / (5.f*std::pow(10, 7)) - 1 << " images"; } if ((m_LastImage + 1) % m_BatchSize == 0) { if (m_CurrentlyRecording) { // save the completed batch m_SaveThreads.push_back(std::thread(&USDiPhASImageSource::saveDataThread, this, m_LastBatch, m_RecordedImageCounter, m_SavingName)); ++m_RecordedImageCounter; } //switch to next one currentBatch = (m_LastBatch + 1) %m_BufferBatches; currentImage = 0; } else { currentBatch = m_LastBatch; currentImage = (m_LastImage + 1); } // create new images and initialize them mitk::Image::Pointer imageUS = m_ImagesBuffer[currentBatch][currentImage].second; mitk::Image::Pointer imagePA = m_ImagesBuffer[currentBatch][currentImage].first; switch (m_DataType) { case DataType::Image_uChar: { if (!imagePA->IsInitialized() || imagePA->GetDimension(0) != imageWidth || imagePA->GetDimension(1) != imageHeight || std::abs(imagePA->GetGeometry()->GetSpacing()[0] - m_ImageSpacing[0]) > std::numeric_limits::epsilon() || std::abs(imagePA->GetGeometry()->GetSpacing()[1] - m_ImageSpacing[1]) > std::numeric_limits::epsilon()) { MITK_INFO << "Update buffers for image data"; unsigned int imageDimensions[3]; imageDimensions[0] = imageWidth; imageDimensions[1] = imageHeight; imageDimensions[2] = 1; short* imageData = new short[beamformedLines*beamformedSamples]; for (int b = 0; b (mitk::Image::New(), mitk::Image::New()); m_ImagesBuffer[b][i].first->Initialize(mitk::MakeScalarPixelType(), 3, imageDimensions); m_ImagesBuffer[b][i].second->Initialize(mitk::MakeScalarPixelType(), 3, imageDimensions); m_ImagesBuffer[b][i].first->SetSpacing(m_ImageSpacing); m_ImagesBuffer[b][i].second->SetSpacing(m_ImageSpacing); m_ImagesBuffer[b][i].first->SetImportVolume(imageData, 0, 0, mitk::Image::RtlCopyMemory); m_ImagesBuffer[b][i].second->SetImportVolume(imageData, 0, 0, mitk::Image::RtlCopyMemory); } } delete[] imageData; imageUS = m_ImagesBuffer[currentBatch][currentImage].second; imagePA = m_ImagesBuffer[currentBatch][currentImage].first; } break; } case DataType::Beamformed_Short: { if (!imagePA->IsInitialized() || imagePA->GetDimension(0) != beamformedLines || imagePA->GetDimension(1) != beamformedSamples || std::abs(imagePA->GetGeometry()->GetSpacing()[0] - m_ImageSpacing[0]) > std::numeric_limits::epsilon() || std::abs(imagePA->GetGeometry()->GetSpacing()[1] - m_ImageSpacing[1]) > std::numeric_limits::epsilon()) { MITK_INFO << "Update buffers for beamformed image data"; unsigned int imageDimensions[3]; imageDimensions[0] = beamformedLines; imageDimensions[1] = beamformedSamples; imageDimensions[2] = 1; short* imageData = new short[beamformedLines*beamformedSamples]; for (int b = 0; b (mitk::Image::New(), mitk::Image::New()); m_ImagesBuffer[b][i].first->Initialize(mitk::MakeScalarPixelType(), 3, imageDimensions); m_ImagesBuffer[b][i].second->Initialize(mitk::MakeScalarPixelType(), 3, imageDimensions); m_ImagesBuffer[b][i].first->SetSpacing(m_ImageSpacing); m_ImagesBuffer[b][i].second->SetSpacing(m_ImageSpacing); m_ImagesBuffer[b][i].first->SetImportVolume(imageData, 0, 0, mitk::Image::RtlCopyMemory); m_ImagesBuffer[b][i].second->SetImportVolume(imageData, 0, 0, mitk::Image::RtlCopyMemory); } } delete[] imageData; imageUS = m_ImagesBuffer[currentBatch][currentImage].second; imagePA = m_ImagesBuffer[currentBatch][currentImage].first; } break; } } // write the given buffer into the image switch (m_DataType) { case DataType::Image_uChar: { if (m_Device->GetScanMode().beamformingAlgorithm == (int)Beamforming::Interleaved_OA_US) { imagePA->SetSlice(imageData); imageUS->SetVolume(&imageData[imageHeight*imageWidth]); } else { imageUS->SetVolume(imageData); } break; } case DataType::Beamformed_Short: { mitk::ImageWriteAccessor dataPAAccess(imagePA); mitk::ImageWriteAccessor dataUSAccess(imageUS); short* dataPA = (short*)dataPAAccess.GetData(); short* dataUS = (short*)dataUSAccess.GetData(); size_t pixelsPerImage = beamformedLines * beamformedSamples; if (m_Device->GetScanMode().beamformingAlgorithm == (int)Beamforming::Interleaved_OA_US) { for (unsigned short sample = 0; sample < beamformedSamples; sample++) { for (unsigned short line = 0; line < beamformedLines; line++) { dataPA[sample*beamformedLines + line] = rfDataArrayBeamformed[line*beamformedSamples + sample]; } } for (unsigned short sample = 0; sample < beamformedSamples; sample++) { for (unsigned short line = 0; line < beamformedLines; line++) { dataUS[sample*beamformedLines + line] = rfDataArrayBeamformed[pixelsPerImage + line*beamformedSamples + sample]; } } } else { for (unsigned short sample = 0; sample < beamformedSamples; sample++) { for (unsigned short line = 0; line < beamformedLines; line++) { dataUS[sample*beamformedLines + line] = rfDataArrayBeamformed[line*beamformedSamples + sample]; } } } break; } } if (m_SavingSettings.saveRaw && m_CurrentlyRecording && rfDataChannelData != nullptr) { mitk::Image::Pointer rawImageUS = m_RawImagesBuffer[currentBatch][currentImage].second; mitk::Image::Pointer rawImagePA = m_RawImagesBuffer[currentBatch][currentImage].first; - mitk::Vector3D rawSpacing; rawSpacing[0] = m_Device->GetScanMode().transducerPitchMeter * 1e3; // save in mm rawSpacing[1] = m_Device->GetScanMode().receivePhaseLengthSeconds / channelDataSamplesPerChannel * 1e6; // save in us rawSpacing[2] = 1; if (!rawImagePA->IsInitialized() || rawImagePA->GetDimension(0) != channelDataChannelsPerDataset || rawImagePA->GetDimension(1) != std::ceil((float)channelDataSamplesPerChannel / 2.f) || rawImageUS->GetDimension(1) != channelDataSamplesPerChannel || rawImageUS->GetDimension(2) != channelDataTotalDatasets - 1 || std::abs(rawImagePA->GetGeometry()->GetSpacing()[0] - rawSpacing[0]) > std::numeric_limits::epsilon() || std::abs(rawImagePA->GetGeometry()->GetSpacing()[1] - rawSpacing[1]) > std::numeric_limits::epsilon()) { MITK_INFO << "Update buffers for raw image data"; unsigned int imageDimensionsPA[3]; imageDimensionsPA[0] = channelDataChannelsPerDataset; imageDimensionsPA[1] = std::ceil((float)channelDataSamplesPerChannel / 2.f); imageDimensionsPA[2] = 1; unsigned int imageDimensionsUS[3]; imageDimensionsUS[0] = channelDataChannelsPerDataset; imageDimensionsUS[1] = channelDataSamplesPerChannel; imageDimensionsUS[2] = channelDataTotalDatasets - 1; short* imageData = new short[channelDataChannelsPerDataset*channelDataSamplesPerChannel]; // * (channelDataTotalDatasets - 1)]; - for (int b = 0; b (mitk::Image::New(), mitk::Image::New()); m_RawImagesBuffer[b][i].first->Initialize(mitk::MakeScalarPixelType(), 3, imageDimensionsPA); m_RawImagesBuffer[b][i].second->Initialize(mitk::MakeScalarPixelType(), 3, imageDimensionsUS); m_RawImagesBuffer[b][i].first->SetSpacing(rawSpacing); m_RawImagesBuffer[b][i].second->SetSpacing(rawSpacing); m_RawImagesBuffer[b][i].first->SetImportVolume(imageData, 0, 0, mitk::Image::RtlCopyMemory); // currently US raw Data is not acquired //m_RawImagesBuffer[b][i].second->SetImportVolume(imageData, 0, 0, mitk::Image::RtlCopyMemory); } } delete[] imageData; + + rawImagePA = m_RawImagesBuffer[currentBatch][currentImage].first; + rawImageUS = m_RawImagesBuffer[currentBatch][currentImage].second; } short offset = m_Device->GetScanMode().accumulation * 2048; mitk::ImageWriteAccessor dataPAAccess(rawImagePA); mitk::ImageWriteAccessor dataUSAccess(rawImageUS); short* dataPA = (short*)dataPAAccess.GetData(); short* dataUS = (short*)dataUSAccess.GetData(); size_t pixelsPerImage = channelDataSamplesPerChannel*channelDataChannelsPerDataset; if (m_Device->GetScanMode().beamformingAlgorithm == (int)Beamforming::Interleaved_OA_US) { for (unsigned short sam = 0; sam < std::ceil((float)channelDataSamplesPerChannel / 2.f); ++sam) { for (unsigned short chan = 0; chan < channelDataChannelsPerDataset; ++chan) { dataPA[sam * channelDataChannelsPerDataset + chan] = rfDataChannelData[sam * channelDataChannelsPerDataset + chan] - offset; // this offset in the raw Images is given by the API... } } // currently not used! /*for (unsigned short sam = 0; sam < channelDataSamplesPerChannel; ++sam) { for (unsigned short chan = 0; chan < channelDataChannelsPerDataset; ++chan) { dataUS[sam * channelDataChannelsPerDataset + chan] = rfDataChannelData[pixelsPerImage + sam * channelDataChannelsPerDataset + chan] - offset; // this offset in the raw Images is given by the API... } }*/ } else { // currently not used! /*for (unsigned short sam = 0; sam < channelDataSamplesPerChannel; ++sam) { for (unsigned short chan = 0; chan < channelDataChannelsPerDataset; ++chan) { dataUS[sam * channelDataChannelsPerDataset + chan] = rfDataChannelData[sam * channelDataChannelsPerDataset + chan] - offset; // this offset in the raw Images is given by the API... } }*/ } } m_LastBatch = currentBatch; m_LastImage = currentImage; m_ImageTimestampsBuffer[currentBatch][currentImage] = currentImageTimestamp; } } 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::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; } void mitk::USDiPhASImageSource::SetSavingName(std::string name) { if (name == "") { m_SavingName = "-replace"; } else { m_SavingName = name; } } // 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) { if (m_SavingSettings.saveRaw) { m_Device->GetScanMode().transferChannelData = true; m_Device->UpdateScanmode(); // set the raw Data to be transfered } m_RecordedImageCounter = 0; // tell the callback to start recording images m_CurrentlyRecording = true; //save the settings! // get the time and date time_t time = std::time(nullptr); time_t* timeptr = &time; std::string currentDate = std::ctime(timeptr); replaceAll(currentDate, ":", "-"); currentDate.pop_back(); if (m_SavingName == "-replace") { m_SavingName = "c:\\ImageData\\" + currentDate; } std::string pathS = m_SavingName + ".settings" + ".txt"; 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(); } // save images, end recording, and clean up else { m_CurrentlyRecording = false; // wait for all saving Threads to finish for (size_t i = 0; i < m_SaveThreads.size(); ++i) { m_SaveThreads[i].join(); } // make sure raw Channel Data is not transferred anymore m_Device->GetScanMode().transferChannelData = false; m_Device->UpdateScanmode(); // clear the save threads m_SaveThreads.clear(); // clean up all threads m_SavingName = "-replace"; } } void mitk::USDiPhASImageSource::OrderImagesInterleaved(Image::Pointer PAImage, Image::Pointer USImage, std::vector> recordedList, bool raw) { unsigned int width = 32; unsigned int heightPA = 32; unsigned int heightUS = 32; unsigned int events = m_Device->GetScanMode().transmitEventsCount; if (!raw) events = 1; // the beamformed image array contains only the resulting image of multiple events if (raw) { width = recordedList.at(0).first->GetDimension(0); heightPA = recordedList.at(0).first->GetDimension(1); heightUS = recordedList.at(0).second->GetDimension(1); } else if (m_DataType == DataType::Beamformed_Short) { width = m_Device->GetScanMode().reconstructionLines; heightPA = m_Device->GetScanMode().reconstructionSamplesPerLine; heightUS = m_Device->GetScanMode().reconstructionSamplesPerLine; } else if (m_DataType == DataType::Image_uChar) { width = m_Device->GetScanMode().imageWidth; heightPA = m_Device->GetScanMode().imageHeight; heightUS = m_Device->GetScanMode().imageHeight; } unsigned int dimPA[] = { width, heightPA, (unsigned int)recordedList.size()}; unsigned int dimUS[] = { width, heightUS, (unsigned int)(recordedList.size() * events)}; PAImage->Initialize(recordedList.back().first->GetPixelType(), 3, dimPA); PAImage->SetSpacing(recordedList.back().first->GetGeometry()->GetSpacing()); USImage->Initialize(recordedList.back().first->GetPixelType(), 3, dimUS); USImage->SetSpacing(recordedList.back().first->GetGeometry()->GetSpacing()); for (int index = 0; index < recordedList.size(); ++index) { mitk::ImageReadAccessor inputReadAccessorPA(recordedList.at(index).first); PAImage->SetSlice(inputReadAccessorPA.GetData(), index); - for (unsigned int i = 0; i < events; ++i) + if (!raw) { - if (raw) - break; // we dont need to go through here in case of raw US data for now - mitk::ImageReadAccessor inputReadAccessorUS(recordedList.at(index).second, recordedList.at(index).second->GetSliceData(i)); - USImage->SetSlice(inputReadAccessorUS.GetData(), index + i); + for (unsigned int i = 0; i < events; ++i) + { + mitk::ImageReadAccessor inputReadAccessorUS(recordedList.at(index).second, recordedList.at(index).second->GetSliceData(i)); + USImage->SetSlice(inputReadAccessorUS.GetData(), index + i); + } } } } 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[] = { width, height, (unsigned int)(recordedList.size() * events) }; USImage->Initialize(recordedList.back().second->GetPixelType(), 3, dimSound); USImage->SetSpacing(recordedList.back().second->GetGeometry()->GetSpacing()); for (int index = 0; index < recordedList.size(); ++index) { for (unsigned int i = 0; i < events; ++i) { mitk::ImageReadAccessor inputReadAccessorUS(recordedList.at(index).second, recordedList.at(index).second->GetSliceData(i)); USImage->SetSlice(inputReadAccessorUS.GetData(), index + i); } } } void mitk::USDiPhASImageSource::saveDataThread(size_t batch, unsigned long long counter, std::string currentSaveName) { char postfix[25]; sprintf(postfix, "%07llu", counter); // initialize file paths and the images Image::Pointer PAImage = Image::New(); Image::Pointer USImage = Image::New(); std::string pathPA = currentSaveName + ".PA.bf." + postfix + ".nrrd"; std::string pathUS = currentSaveName + ".US.bf." + postfix + ".nrrd"; std::string pathTS = currentSaveName + ".ts." + postfix + ".csv"; // raw Images (if chosen to be saved) Image::Pointer PAImageRaw = Image::New(); Image::Pointer USImageRaw = Image::New(); std::string pathPARaw = currentSaveName + ".PA.rf." + postfix + ".nrrd"; std::string pathUSRaw = currentSaveName + ".US.rf." + postfix + ".nrrd"; if (m_Device->GetScanMode().beamformingAlgorithm == (int)Beamforming::Interleaved_OA_US) // save a PAImage if we used interleaved mode { // first, save the pyro data m_Pyro->SaveData(currentSaveName + ".pyro." + postfix + ".csv"); // now order the images and save them // the beamformed ones... OrderImagesInterleaved(PAImage, USImage, m_ImagesBuffer[batch], false); mitk::IOUtil::Save(USImage, pathUS); if (m_SavingSettings.saveBeamformed) { mitk::IOUtil::Save(PAImage, pathPA); } // ...and the raw images if (m_SavingSettings.saveRaw) { OrderImagesInterleaved(PAImageRaw, USImageRaw, m_RawImagesBuffer[batch], true); // mitk::IOUtil::Save(USImageRaw, pathUSRaw); mitk::IOUtil::Save(PAImageRaw, pathPARaw); } // save the timestamps! ofstream timestampFile; timestampFile.open(pathTS); timestampFile << ",timestamp"; // write the header for (size_t index = 0; index < m_ImageTimestampsBuffer[batch].size(); ++index) { timestampFile << "\n" << index << "," << m_ImageTimestampsBuffer[batch][index]; } timestampFile.close(); } else if (m_Device->GetScanMode().beamformingAlgorithm == (int)Beamforming::PlaneWaveCompound) // save no PAImage if we used US only mode { OrderImagesUltrasound(USImage, m_ImagesBuffer[batch]); mitk::IOUtil::Save(USImage, pathUS); } MITK_INFO << "The saving Thread for batch " << batch << " has finished."; } \ No newline at end of file diff --git a/Modules/USUI/Qmitk/QmitkUSControlsCustomDiPhASDeviceWidget.cpp b/Modules/USUI/Qmitk/QmitkUSControlsCustomDiPhASDeviceWidget.cpp index ec545dbccf..ac8c62cdad 100644 --- a/Modules/USUI/Qmitk/QmitkUSControlsCustomDiPhASDeviceWidget.cpp +++ b/Modules/USUI/Qmitk/QmitkUSControlsCustomDiPhASDeviceWidget.cpp @@ -1,472 +1,470 @@ /*=================================================================== 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 "QmitkUSControlsCustomDiPhASDeviceWidget.h" #include "ui_QmitkUSControlsCustomDiPhASDeviceWidget.h" #include #include QmitkUSControlsCustomDiPhASDeviceWidget::QmitkUSControlsCustomDiPhASDeviceWidget(QWidget *parent) : QmitkUSAbstractCustomWidget(parent), ui(new Ui::QmitkUSControlsCustomDiPhASDeviceWidget) { } QmitkUSControlsCustomDiPhASDeviceWidget::QmitkUSControlsCustomDiPhASDeviceWidget() : ui(new Ui::QmitkUSControlsCustomDiPhASDeviceWidget) { } QmitkUSControlsCustomDiPhASDeviceWidget::~QmitkUSControlsCustomDiPhASDeviceWidget() { m_ControlInterface = dynamic_cast (this->GetDevice()->GetControlInterfaceCustom().GetPointer()); delete ui; } std::string QmitkUSControlsCustomDiPhASDeviceWidget::GetDeviceClass() const { return "org.mitk.modules.us.USDiPhASDevice"; } QmitkUSAbstractCustomWidget* QmitkUSControlsCustomDiPhASDeviceWidget::Clone(QWidget* parent) const { QmitkUSAbstractCustomWidget* clonedWidget = new QmitkUSControlsCustomDiPhASDeviceWidget(parent); clonedWidget->SetDevice(this->GetDevice()); return clonedWidget; } void QmitkUSControlsCustomDiPhASDeviceWidget::OnDeviceSet() { m_ControlInterface = dynamic_cast (this->GetDevice()->GetControlInterfaceCustom().GetPointer()); if ( m_ControlInterface.IsNull() ) { MITK_WARN("QmitkUSAbstractCustomWidget")("QmitkUSControlsCustomDiPhASDeviceWidget") << "Did not get a custom device control interface."; } //now pass the default values m_OldReconstructionLines = 0; m_ControlInterface->SetSilentUpdate(true); // don't update the scanmode everytime OnTransmitPhaseLengthChanged(); OnExcitationFrequencyChanged(); OnTransmitEventsChanged(); OnVoltageChanged(); OnScanDepthChanged(); // HERE OnAveragingCountChanged(); OnTGCChanged(); OnDataTypeChanged(); OnPitchChanged(); OnReconstructedSamplesChanged(); OnReconstructedLinesChanged(); OnSpeedOfSoundChanged(); OnBandpassEnabledChanged(); OnLowCutChanged(); OnHighCutChanged(); OnUseBModeFilterChanged(); // HERE OnVerticalSpacingChanged(); OnScatteringCoefficientChanged(); OnCompensateScatteringChanged(); OnChangedSavingSettings(); OnCompensateEnergyChanged(); OnSaveNameChanged(); m_ControlInterface->SetSilentUpdate(false); // on the last update pass the scanmode and geometry! OnModeChanged(); // HERE } void QmitkUSControlsCustomDiPhASDeviceWidget::Initialize() { ui->setupUi(this); connect(ui->CompensateEnergy, SIGNAL(stateChanged(int)), this, SLOT(OnCompensateEnergyChanged())); connect(ui->UseBModeFilter, SIGNAL(stateChanged(int)), this, SLOT(OnUseBModeFilterChanged())); connect(ui->StartStopRecord, SIGNAL(clicked()), this, SLOT(OnRecordChanged())); connect(ui->ScatteringCoefficient, SIGNAL(valueChanged(int)), this, SLOT(OnScatteringCoefficientChanged())); connect(ui->CompensateScattering, SIGNAL(stateChanged(int)), this, SLOT(OnCompensateScatteringChanged())); connect(ui->VerticalSpacing, SIGNAL(valueChanged(double)), this, SLOT(OnVerticalSpacingChanged())); connect(ui->SaveBeamformed, SIGNAL(stateChanged(int)), this, SLOT(OnChangedSavingSettings())); connect(ui->SaveRaw, SIGNAL(stateChanged(int)), this, SLOT(OnChangedSavingSettings())); //transmit connect(ui->TransmitPhaseLength, SIGNAL(valueChanged(double)), this, SLOT(OnTransmitPhaseLengthChanged())); connect(ui->ExcitationFrequency, SIGNAL(valueChanged(double)), this, SLOT(OnExcitationFrequencyChanged())); connect(ui->TransmitEvents, SIGNAL(valueChanged(int)), this, SLOT(OnTransmitEventsChanged())); connect(ui->Voltage, SIGNAL(valueChanged(int)), this, SLOT(OnVoltageChanged())); connect(ui->Mode, SIGNAL(currentTextChanged(QString)), this, SLOT(OnModeChanged())); //Receive connect(ui->ScanDepth, SIGNAL(valueChanged(double)), this, SLOT(OnScanDepthChanged())); connect(ui->AveragingCount, SIGNAL(valueChanged(int)), this, SLOT(OnAveragingCountChanged())); connect(ui->TimeGainCompensation0Slider, SIGNAL(valueChanged(int)), this, SLOT(OnTGCChanged())); connect(ui->TimeGainCompensation1Slider, SIGNAL(valueChanged(int)), this, SLOT(OnTGCChanged())); connect(ui->TimeGainCompensation2Slider, SIGNAL(valueChanged(int)), this, SLOT(OnTGCChanged())); connect(ui->TimeGainCompensation3Slider, SIGNAL(valueChanged(int)), this, SLOT(OnTGCChanged())); connect(ui->TimeGainCompensation4Slider, SIGNAL(valueChanged(int)), this, SLOT(OnTGCChanged())); connect(ui->TimeGainCompensation5Slider, SIGNAL(valueChanged(int)), this, SLOT(OnTGCChanged())); connect(ui->TimeGainCompensation6Slider, SIGNAL(valueChanged(int)), this, SLOT(OnTGCChanged())); connect(ui->TimeGainCompensation7Slider, SIGNAL(valueChanged(int)), this, SLOT(OnTGCChanged())); connect(ui->DataType, SIGNAL(currentTextChanged(QString)), this, SLOT(OnDataTypeChanged())); //Beamforming connect(ui->PitchOfTransducer, SIGNAL(valueChanged(double)), this, SLOT(OnPitchChanged())); connect(ui->ReconstructedSamplesPerLine, SIGNAL(valueChanged(int)), this, SLOT(OnReconstructedSamplesChanged())); connect(ui->ReconstructedLines, SIGNAL(valueChanged(int)), this, SLOT(OnReconstructedLinesChanged())); connect(ui->SpeedOfSound, SIGNAL(valueChanged(int)), this, SLOT(OnSpeedOfSoundChanged())); //Bandpass connect(ui->BandpassEnabled, SIGNAL(currentTextChanged(QString)), this, SLOT(OnBandpassEnabledChanged())); connect(ui->LowCut, SIGNAL(valueChanged(double)), this, SLOT(OnLowCutChanged())); connect(ui->HighCut, SIGNAL(valueChanged(double)), this, SLOT(OnHighCutChanged())); connect(ui->RecordingName, SIGNAL(textChanged()), this, SLOT(OnSaveNameChanged())); } //slots void QmitkUSControlsCustomDiPhASDeviceWidget::OnCompensateEnergyChanged() { if (m_ControlInterface.IsNull()) { return; } bool CompensateEnergy = ui->CompensateEnergy->isChecked(); m_ControlInterface->SetCompensateEnergy(CompensateEnergy); } void QmitkUSControlsCustomDiPhASDeviceWidget::OnUseBModeFilterChanged() { if (m_ControlInterface.IsNull()) { return; } bool UseBModeFilter = ui->UseBModeFilter->isChecked(); m_ControlInterface->SetUseBModeFilter(UseBModeFilter); } void QmitkUSControlsCustomDiPhASDeviceWidget::OnSaveNameChanged() { if (m_ControlInterface.IsNull()) { return; } m_ControlInterface->SetSavingName(ui->RecordingName->toPlainText().toStdString()); } void QmitkUSControlsCustomDiPhASDeviceWidget::OnRecordChanged() { if (m_ControlInterface.IsNull()) { return; } if (ui->StartStopRecord->text() == "Start Recording") { ui->StartStopRecord->setText("Stop Recording"); ui->UseBModeFilter->setEnabled(false); ui->ScatteringCoefficient->setEnabled(false); ui->CompensateScattering->setEnabled(false); ui->VerticalSpacing->setEnabled(false); ui->SaveBeamformed->setEnabled(false); ui->SaveRaw->setEnabled(false); ui->TransmitPhaseLength->setEnabled(false); ui->ExcitationFrequency->setEnabled(false); ui->TransmitEvents->setEnabled(false); ui->Voltage->setEnabled(false); ui->Mode->setEnabled(false); ui->ScanDepth->setEnabled(false); ui->AveragingCount->setEnabled(false); ui->TimeGainCompensation0Slider->setEnabled(false); ui->TimeGainCompensation1Slider->setEnabled(false); ui->TimeGainCompensation2Slider->setEnabled(false); ui->TimeGainCompensation3Slider->setEnabled(false); ui->TimeGainCompensation4Slider->setEnabled(false); ui->TimeGainCompensation5Slider->setEnabled(false); ui->TimeGainCompensation6Slider->setEnabled(false); ui->TimeGainCompensation7Slider->setEnabled(false); ui->DataType->setEnabled(false); ui->PitchOfTransducer->setEnabled(false); ui->ReconstructedSamplesPerLine->setEnabled(false); ui->ReconstructedLines->setEnabled(false); ui->SpeedOfSound->setEnabled(false); ui->BandpassEnabled->setEnabled(false); ui->LowCut->setEnabled(false); ui->HighCut->setEnabled(false); ui->CompensateEnergy->setEnabled(false); ui->RecordingName->setEnabled(false); m_ControlInterface->SetRecord(true); } else { ui->StartStopRecord->setText("Start Recording"); ui->UseBModeFilter->setEnabled(true); ui->CompensateScattering->setEnabled(true); if(ui->CompensateScattering->isChecked()) ui->ScatteringCoefficient->setEnabled(true); ui->VerticalSpacing->setEnabled(true); ui->SaveBeamformed->setEnabled(true); ui->SaveRaw->setEnabled(true); ui->TransmitPhaseLength->setEnabled(true); ui->ExcitationFrequency->setEnabled(true); ui->TransmitEvents->setEnabled(true); ui->Voltage->setEnabled(true); ui->Mode->setEnabled(true); ui->ScanDepth->setEnabled(true); ui->AveragingCount->setEnabled(true); ui->TimeGainCompensation0Slider->setEnabled(true); ui->TimeGainCompensation1Slider->setEnabled(true); ui->TimeGainCompensation2Slider->setEnabled(true); ui->TimeGainCompensation3Slider->setEnabled(true); ui->TimeGainCompensation4Slider->setEnabled(true); ui->TimeGainCompensation5Slider->setEnabled(true); ui->TimeGainCompensation6Slider->setEnabled(true); ui->TimeGainCompensation7Slider->setEnabled(true); ui->DataType->setEnabled(true); ui->PitchOfTransducer->setEnabled(true); ui->ReconstructedSamplesPerLine->setEnabled(true); ui->ReconstructedLines->setEnabled(true); ui->SpeedOfSound->setEnabled(true); ui->BandpassEnabled->setEnabled(true); ui->LowCut->setEnabled(true); ui->HighCut->setEnabled(true); ui->CompensateEnergy->setEnabled(true); ui->RecordingName->setEnabled(true); m_ControlInterface->SetRecord(false); size_t index_ = ui->RecordingName->toPlainText().toStdString().find_last_of('_'); if (std::string::npos == index_) ui->RecordingName->setPlainText(ui->RecordingName->toPlainText() + "_1"); else { std::string oldName = ui->RecordingName->toPlainText().toStdString(); int number = std::stoi(oldName.substr(index_ + 1, oldName.length() - index_)) + 1; std::string newName = oldName.substr(0, index_ + 1) + std::to_string(number); ui->RecordingName->setPlainText(QString::fromStdString(newName)); } } } void QmitkUSControlsCustomDiPhASDeviceWidget::OnVerticalSpacingChanged() { if (m_ControlInterface.IsNull()) { return; } m_ControlInterface->SetVerticalSpacing(ui->VerticalSpacing->value()); } void QmitkUSControlsCustomDiPhASDeviceWidget::OnScatteringCoefficientChanged() { if (m_ControlInterface.IsNull()) { return; } m_ControlInterface->SetScatteringCoefficient(ui->ScatteringCoefficient->value()); } void QmitkUSControlsCustomDiPhASDeviceWidget::OnCompensateScatteringChanged() { if (m_ControlInterface.IsNull()) { return; } if (ui->CompensateScattering->isChecked()) ui->ScatteringCoefficient->setEnabled(true); else ui->ScatteringCoefficient->setEnabled(false); m_ControlInterface->SetCompensateScattering(ui->CompensateScattering->isChecked()); } void QmitkUSControlsCustomDiPhASDeviceWidget::OnChangedSavingSettings() { if (m_ControlInterface.IsNull()) { return; } mitk::USDiPhASDeviceCustomControls::SavingSettings settings; settings.saveBeamformed = ui->SaveBeamformed->isChecked(); settings.saveRaw = ui->SaveRaw->isChecked(); m_ControlInterface->SetSavingSettings(settings); } //Transmit void QmitkUSControlsCustomDiPhASDeviceWidget::OnTransmitPhaseLengthChanged() { if (m_ControlInterface.IsNull()) { return; } m_ControlInterface->SetTransmitPhaseLength(ui->TransmitPhaseLength->value()); } void QmitkUSControlsCustomDiPhASDeviceWidget::OnExcitationFrequencyChanged() { if (m_ControlInterface.IsNull()) { return; } m_ControlInterface->SetExcitationFrequency(ui->ExcitationFrequency->value()); } void QmitkUSControlsCustomDiPhASDeviceWidget::OnTransmitEventsChanged() { if (m_ControlInterface.IsNull()) { return; } if (ui->TransmitEvents->value()%2 == 0 || ui->TransmitEvents->value() > 11) ui->TransmitEvents->setValue(1); m_ControlInterface->SetTransmitEvents(ui->TransmitEvents->value()); } void QmitkUSControlsCustomDiPhASDeviceWidget::OnVoltageChanged() { if (m_ControlInterface.IsNull()) { return; } m_ControlInterface->SetVoltage(ui->Voltage->value()); } void QmitkUSControlsCustomDiPhASDeviceWidget::OnModeChanged() { if (m_ControlInterface.IsNull()) { return; } QString Mode = ui->Mode->currentText(); bool silent = m_ControlInterface->GetSilentUpdate(); m_ControlInterface->SetSilentUpdate(true); if (Mode == "Ultrasound only") { m_ControlInterface->SetMode(false); - ui->TransmitEvents->setValue(1); } else if (Mode == "Interleaved") { m_ControlInterface->SetMode(true); - ui->TransmitEvents->setValue(1); } if (!silent) { m_ControlInterface->SetSilentUpdate(false); } OnTransmitEventsChanged(); } //Receive void QmitkUSControlsCustomDiPhASDeviceWidget::OnScanDepthChanged() { if (m_ControlInterface.IsNull()) { return; } m_ControlInterface->SetScanDepth(ui->ScanDepth->value()); } void QmitkUSControlsCustomDiPhASDeviceWidget::OnAveragingCountChanged() { if (m_ControlInterface.IsNull()) { return; } m_ControlInterface->SetAveragingCount(ui->AveragingCount->value()); } void QmitkUSControlsCustomDiPhASDeviceWidget::OnTGCChanged() { if (m_ControlInterface.IsNull()) { return; } int tgc[8]; tgc[0] = ui->TimeGainCompensation0Slider->value(); tgc[1] = ui->TimeGainCompensation1Slider->value(); tgc[2] = ui->TimeGainCompensation2Slider->value(); tgc[3] = ui->TimeGainCompensation3Slider->value(); tgc[4] = ui->TimeGainCompensation4Slider->value(); tgc[5] = ui->TimeGainCompensation5Slider->value(); tgc[6] = ui->TimeGainCompensation6Slider->value(); tgc[7] = ui->TimeGainCompensation7Slider->value(); QString label[8]; label[0] = QString::fromStdString(std::to_string(ui->TimeGainCompensation0Slider->value())); label[1] = QString::fromStdString(std::to_string(ui->TimeGainCompensation1Slider->value())); label[2] = QString::fromStdString(std::to_string(ui->TimeGainCompensation2Slider->value())); label[3] = QString::fromStdString(std::to_string(ui->TimeGainCompensation3Slider->value())); label[4] = QString::fromStdString(std::to_string(ui->TimeGainCompensation4Slider->value())); label[5] = QString::fromStdString(std::to_string(ui->TimeGainCompensation5Slider->value())); label[6] = QString::fromStdString(std::to_string(ui->TimeGainCompensation6Slider->value())); label[7] = QString::fromStdString(std::to_string(ui->TimeGainCompensation7Slider->value())); ui->TimeGainCompensation0Label->setText(label[0]); ui->TimeGainCompensation1Label->setText(label[1]); ui->TimeGainCompensation2Label->setText(label[2]); ui->TimeGainCompensation3Label->setText(label[3]); ui->TimeGainCompensation4Label->setText(label[4]); ui->TimeGainCompensation5Label->setText(label[5]); ui->TimeGainCompensation6Label->setText(label[6]); ui->TimeGainCompensation7Label->setText(label[7]); ui->BandpassLabel->hide(); ui->BandpassParameters->setEnabled(false); ui->Mode->hide(); ui->ModeLabel->hide(); m_ControlInterface->SetTGC(tgc); } void QmitkUSControlsCustomDiPhASDeviceWidget::OnDataTypeChanged() { if (m_ControlInterface.IsNull()) { return; } QString DataType = ui->DataType->currentText(); if (DataType == "Image Data") { m_ControlInterface->SetDataType(mitk::USDiPhASDeviceCustomControls::DataType::Image_uChar); } else if (DataType == "Beamformed Data") { m_ControlInterface->SetDataType(mitk::USDiPhASDeviceCustomControls::DataType::Beamformed_Short); } } //Beamforming void QmitkUSControlsCustomDiPhASDeviceWidget::OnPitchChanged() { if (m_ControlInterface.IsNull()) { return; } m_ControlInterface->SetPitch(ui->PitchOfTransducer->value()); } void QmitkUSControlsCustomDiPhASDeviceWidget::OnReconstructedSamplesChanged() { if (m_ControlInterface.IsNull()) { return; } if(ui->ReconstructedSamplesPerLine->value()%256 != 0) ui->ReconstructedSamplesPerLine->setValue(2048); m_ControlInterface->SetReconstructedSamples(ui->ReconstructedSamplesPerLine->value()); } void QmitkUSControlsCustomDiPhASDeviceWidget::OnReconstructedLinesChanged() { if (m_ControlInterface.IsNull()) { return; } if (m_OldReconstructionLines == 0) m_OldReconstructionLines = ui->ReconstructedLines->value(); if(ui->ReconstructedLines->value()%128 != 0) ui->ReconstructedLines->setValue(128); m_ControlInterface->SetReconstructedLines(ui->ReconstructedLines->value()); ui->PitchOfTransducer->setValue(ui->PitchOfTransducer->value()*((double)m_OldReconstructionLines / (double)ui->ReconstructedLines->value())); m_OldReconstructionLines = ui->ReconstructedLines->value(); } void QmitkUSControlsCustomDiPhASDeviceWidget::OnSpeedOfSoundChanged() { if (m_ControlInterface.IsNull()) { return; } m_ControlInterface->SetSpeedOfSound(ui->SpeedOfSound->value()); } //Bandpass void QmitkUSControlsCustomDiPhASDeviceWidget::OnBandpassEnabledChanged() { if (m_ControlInterface.IsNull()) { return; } if (ui->BandpassEnabled->currentText() == "On") { m_ControlInterface->SetBandpassEnabled(true); } else { m_ControlInterface->SetBandpassEnabled(false); } } void QmitkUSControlsCustomDiPhASDeviceWidget::OnLowCutChanged() { if (m_ControlInterface.IsNull()) { return; } unsigned int Low = ui->LowCut->value(); unsigned int High = ui->HighCut->value(); if (Low > High) { ui->LowCut->setValue(High); MITK_INFO << "User tried to set LowCut>HighCut."; } m_ControlInterface->SetLowCut(ui->LowCut->value()); } void QmitkUSControlsCustomDiPhASDeviceWidget::OnHighCutChanged() { if (m_ControlInterface.IsNull()) { return; } unsigned int Low = ui->LowCut->value(); unsigned int High = ui->HighCut->value(); if (Low > High) { ui->HighCut->setValue(Low); MITK_INFO << "User tried to set LowCut>HighCut."; } m_ControlInterface->SetHighCut(ui->HighCut->value()); } diff --git a/Modules/USUI/Qmitk/QmitkUSControlsCustomDiPhASDeviceWidget.ui b/Modules/USUI/Qmitk/QmitkUSControlsCustomDiPhASDeviceWidget.ui index f1814dc222..2e114f54da 100644 --- a/Modules/USUI/Qmitk/QmitkUSControlsCustomDiPhASDeviceWidget.ui +++ b/Modules/USUI/Qmitk/QmitkUSControlsCustomDiPhASDeviceWidget.ui @@ -1,797 +1,797 @@ QmitkUSControlsCustomDiPhASDeviceWidget 0 0 351 - 974 + 993 Form <html><head/><body><p><span style=" font-weight:600;">Record Images</span></p></body></html> Save PA Beamformed false Save PA Raw true 250 50 E:/ImageData/recordingName 100 25 Start Recording Qt::Horizontal 40 20 <html><head/><body><p><span style=" font-weight:600;">Beamforming Parameters</span></p></body></html> 256 4096 256 2048 3 0.005000000000000 10.000000000000000 0.005000000000000 0.150000000000000 Qt::PreventContextMenu 128 1024 128 256 Samples per Line Reconstructed Lines 1000 1000000 5 - 1480 + 1540 Speed of Sound [m/s] Pitch of Transducer [mm] <html><head/><body><p><span style=" font-weight:600;">Receive Parameters</span></p></body></html> 1 100 1 Scan Depth [mm] Averaging Count TGC Max 42 42 Qt::Horizontal 0 TGC Min 42 42 Qt::Horizontal false Beamformed Data Image Data DataType 3.000000000000000 200.000000000000000 - 40.000000000000000 + 50.000000000000000 42 38 Qt::Horizontal TextLabel 42 34 Qt::Horizontal 42 42 Qt::Horizontal 42 40 Qt::Horizontal 42 36 Qt::Horizontal TextLabel TextLabel TextLabel TextLabel TextLabel 0 0 0 0 16777215 16777215 42 - 0 + 32 Qt::Horizontal <html><head/><body><p><span style=" font-weight:600;">Time Gain Compensation</span></p></body></html> true Compensate Fluence For Scattering true 5 25 15 false Avg. μs' [1/cm] <html><head/><body><p><span style=" font-weight:600;">Display Parameters</span></p></body></html> Envelope Filter true false Compensate Energy Values 0.010000000000000 1.200000000000000 0.050000000000000 0.100000000000000 Vertical Spacing <html><head/><body><p><span style=" font-weight:600;">Transmit Parameters</span></p></body></html> 1.000000000000000 15.000000000000000 0.100000000000000 7.500000000000000 1 11 2 3 Transmit Events true false 1 1.000000000000000 10000.000000000000000 4.000000000000000 Transmit Phase Length [us] Excitation Frequency [MHz] false Interleaved Ultrasound only false 0 75 - 5 + 10 Voltage [V] Mode false <html><head/><body><p><span style=" font-weight:600;">Bandpass Parameters</span></p></body></html> false High Cut [MHz] false Low Cut [MHz] false Bandpass Enabled false false 5.000000000000000 false Off On Qt::Vertical 20 40