diff --git a/Modules/US/USNavigation/mitkUSCombinedModality.cpp b/Modules/US/USNavigation/mitkUSCombinedModality.cpp index 23d7352956..917c40ce3e 100644 --- a/Modules/US/USNavigation/mitkUSCombinedModality.cpp +++ b/Modules/US/USNavigation/mitkUSCombinedModality.cpp @@ -1,555 +1,555 @@ /*=================================================================== 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 "mitkUSCombinedModality.h" #include "mitkUSDevice.h" #include "mitkNavigationDataSource.h" #include "mitkImageReadAccessor.h" #include #include #include "mitkTrackingDeviceSource.h" // US Control Interfaces #include "mitkUSControlInterfaceProbes.h" #include "mitkUSControlInterfaceBMode.h" #include "mitkUSControlInterfaceDoppler.h" #include //TempIncludes #include const std::string mitk::USCombinedModality::DeviceClassIdentifier = "org.mitk.modules.us.USCombinedModality"; const char* mitk::USCombinedModality::DefaultProbeIdentifier = "default"; const char* mitk::USCombinedModality::ProbeAndDepthSeperator = "_"; mitk::USCombinedModality::USCombinedModality(USDevice::Pointer usDevice, NavigationDataSource::Pointer trackingDevice, std::string manufacturer, std::string model) : mitk::USDevice(manufacturer, model), m_UltrasoundDevice(usDevice), m_TrackingDevice(trackingDevice), m_SmoothingFilter(mitk::NavigationDataSmoothingFilter::New()), m_DelayFilter(mitk::NavigationDataDelayFilter::New(0)), m_NumberOfSmoothingValues(0), m_DelayCount(0) { this->RebuildFilterPipeline(); //create a new output (for the image data) mitk::Image::Pointer newOutput = mitk::Image::New(); this->SetNthOutput(0,newOutput); // Combined Modality should not spawn an own acquire thread, because // image acquiring is done by the included us device this->SetSpawnAcquireThread(false); } mitk::USCombinedModality::~USCombinedModality() { } std::string mitk::USCombinedModality::GetDeviceClass() { return DeviceClassIdentifier; } mitk::USImageSource::Pointer mitk::USCombinedModality::GetUSImageSource() { if (m_UltrasoundDevice.IsNull()) { MITK_ERROR("USCombinedModality")("USDevice") << "UltrasoundDevice must not be null."; mitkThrow() << "UltrasoundDevice must not be null."; } return m_UltrasoundDevice->GetUSImageSource(); } mitk::USAbstractControlInterface::Pointer mitk::USCombinedModality::GetControlInterfaceCustom() { if (m_UltrasoundDevice.IsNull()) { MITK_ERROR("USCombinedModality")("USDevice") << "UltrasoundDevice must not be null."; mitkThrow() << "UltrasoundDevice must not be null."; } return m_UltrasoundDevice->GetControlInterfaceCustom(); } mitk::USControlInterfaceBMode::Pointer mitk::USCombinedModality::GetControlInterfaceBMode() { if (m_UltrasoundDevice.IsNull()) { MITK_ERROR("USCombinedModality")("USDevice") << "UltrasoundDevice must not be null."; mitkThrow() << "UltrasoundDevice must not be null."; } return m_UltrasoundDevice->GetControlInterfaceBMode(); } mitk::USControlInterfaceProbes::Pointer mitk::USCombinedModality::GetControlInterfaceProbes() { if (m_UltrasoundDevice.IsNull()) { MITK_ERROR("USCombinedModality")("USDevice") << "UltrasoundDevice must not be null."; mitkThrow() << "UltrasoundDevice must not be null."; } return m_UltrasoundDevice->GetControlInterfaceProbes(); } mitk::USControlInterfaceDoppler::Pointer mitk::USCombinedModality::GetControlInterfaceDoppler() { if (m_UltrasoundDevice.IsNull()) { MITK_ERROR("USCombinedModality")("USDevice") << "UltrasoundDevice must not be null."; mitkThrow() << "UltrasoundDevice must not be null."; } return m_UltrasoundDevice->GetControlInterfaceDoppler(); } void mitk::USCombinedModality::UnregisterOnService() { if (m_DeviceState == State_Activated) { this->Deactivate(); } if (m_DeviceState == State_Connected) { this->Disconnect(); } mitk::USDevice::UnregisterOnService(); } mitk::AffineTransform3D::Pointer mitk::USCombinedModality::GetCalibration() { return this->GetCalibration(this->GetCurrentDepthValue(), this->GetIdentifierForCurrentProbe()); } mitk::AffineTransform3D::Pointer mitk::USCombinedModality::GetCalibration(std::string depth) { return this->GetCalibration(depth, this->GetIdentifierForCurrentProbe()); } mitk::AffineTransform3D::Pointer mitk::USCombinedModality::GetCalibration(std::string depth, std::string probe) { // make sure that there is no '/' which would cause problems for TinyXML std::replace(probe.begin(), probe.end(), '/', '-'); // create identifier for calibration from probe and depth std::string calibrationKey = probe + mitk::USCombinedModality::ProbeAndDepthSeperator + depth; // find calibration for combination of probe identifier and depth std::map::iterator calibrationIterator = m_Calibrations.find(calibrationKey); if (calibrationIterator == m_Calibrations.end()) { MITK_INFO("USCombinedModality")("USDevice") << "No calibration found for selected probe and depth."; return 0; } return calibrationIterator->second; } void mitk::USCombinedModality::SetCalibration (mitk::AffineTransform3D::Pointer calibration) { if (calibration.IsNull()) { MITK_WARN << "Null pointer passed to SetCalibration of mitk::USDevice. Ignoring call."; return; } std::string calibrationKey = this->GetIdentifierForCurrentCalibration(); if (calibrationKey.empty()) { MITK_WARN << "Could not get a key for the calibration -> Calibration cannot be set."; return; } m_Calibrations[calibrationKey] = calibration; if (m_ServiceRegistration != 0) { this->UpdateServiceProperty(mitk::USImageMetadata::PROP_DEV_ISCALIBRATED, true); } } bool mitk::USCombinedModality::RemoveCalibration() { return this->RemoveCalibration(this->GetCurrentDepthValue(), this->GetIdentifierForCurrentProbe()); } bool mitk::USCombinedModality::RemoveCalibration(std::string depth) { return this->RemoveCalibration(depth, this->GetIdentifierForCurrentProbe()); } bool mitk::USCombinedModality::RemoveCalibration(std::string depth, std::string probe) { // make sure that there is no '/' which would cause problems for TinyXML std::replace(probe.begin(), probe.end(), '/', '-'); // create identifier for calibration from probe and depth std::string calibrationKey = probe + mitk::USCombinedModality::ProbeAndDepthSeperator + depth; return m_Calibrations.erase(calibrationKey) > 0; } void mitk::USCombinedModality::SetNumberOfSmoothingValues(unsigned int numberOfSmoothingValues) { unsigned int oldNumber = m_NumberOfSmoothingValues; m_NumberOfSmoothingValues = numberOfSmoothingValues; // if filter should be activated or deactivated if ( ( oldNumber == 0 && numberOfSmoothingValues != 0 ) || ( oldNumber != 0 && numberOfSmoothingValues == 0 ) ) { this->RebuildFilterPipeline(); } m_SmoothingFilter->SetNumerOfValues(numberOfSmoothingValues); } void mitk::USCombinedModality::SetDelayCount(unsigned int delayCount) { unsigned int oldCount = m_DelayCount; m_DelayCount = delayCount; // if filter should be activated or deactivated if ( ( oldCount == 0 && delayCount != 0 ) || ( oldCount != 0 && delayCount == 0 ) ) { this->RebuildFilterPipeline(); } m_DelayFilter->SetDelay(delayCount); } bool mitk::USCombinedModality::OnInitialization() { if (m_UltrasoundDevice.IsNull()) { MITK_ERROR("USCombinedModality")("USDevice") << "UltrasoundDevice must not be null."; mitkThrow() << "UltrasoundDevice must not be null."; } if ( m_UltrasoundDevice->GetDeviceState() < mitk::USDevice::State_Initialized ) { return m_UltrasoundDevice->Initialize(); } else { return true; } } bool mitk::USCombinedModality::OnConnection() { if (m_UltrasoundDevice.IsNull()) { MITK_ERROR("USCombinedModality")("USDevice") << "UltrasoundDevice must not be null."; mitkThrow() << "UltrasoundDevice must not be null."; } // connect ultrasound device only if it is not already connected if ( m_UltrasoundDevice->GetDeviceState() >= mitk::USDevice::State_Connected ) { return true; } else { return m_UltrasoundDevice->Connect(); } } bool mitk::USCombinedModality::OnDisconnection() { if (m_UltrasoundDevice.IsNull()) { MITK_ERROR("USCombinedModality")("USDevice") << "UltrasoundDevice must not be null."; mitkThrow() << "UltrasoundDevice must not be null."; } return m_UltrasoundDevice->Disconnect(); } bool mitk::USCombinedModality::OnActivation() { if ( m_UltrasoundDevice.IsNull() ) { MITK_ERROR("USCombinedModality")("USDevice") << "UltrasoundDevice must not be null."; mitkThrow() << "UltrasoundDevice must not be null."; } mitk::TrackingDeviceSource::Pointer trackingDeviceSource = dynamic_cast(m_TrackingDevice.GetPointer()); if ( trackingDeviceSource.IsNull() ) { MITK_WARN("USCombinedModality")("USDevice") << "Cannot start tracking as TrackingDeviceSource is null."; } trackingDeviceSource->StartTracking(); // activate ultrasound device only if it is not already activated if ( m_UltrasoundDevice->GetDeviceState() >= mitk::USDevice::State_Activated ) { return true; } else { return m_UltrasoundDevice->Activate(); } } bool mitk::USCombinedModality::OnDeactivation() { if ( m_UltrasoundDevice.IsNull() ) { MITK_ERROR("USCombinedModality")("USDevice") << "UltrasoundDevice must not be null."; mitkThrow() << "UltrasoundDevice must not be null."; } mitk::TrackingDeviceSource::Pointer trackingDeviceSource = dynamic_cast(m_TrackingDevice.GetPointer()); if ( trackingDeviceSource.IsNull() ) { MITK_WARN("USCombinedModality")("USDevice") << "Cannot stop tracking as TrackingDeviceSource is null."; } trackingDeviceSource->StopTracking(); m_UltrasoundDevice->Deactivate(); return m_UltrasoundDevice->GetIsConnected(); } void mitk::USCombinedModality::OnFreeze(bool freeze) { if (m_UltrasoundDevice.IsNull()) { MITK_ERROR("USCombinedModality")("USDevice") << "UltrasoundDevice must not be null."; mitkThrow() << "UltrasoundDevice must not be null."; } m_UltrasoundDevice->SetIsFreezed(freeze); mitk::TrackingDeviceSource::Pointer trackingDeviceSource = dynamic_cast(m_TrackingDevice.GetPointer()); if ( trackingDeviceSource.IsNull() ) { MITK_WARN("USCombinedModality")("USDevice") << "Cannot freeze tracking."; } else { if ( freeze ) { trackingDeviceSource->StopTracking(); } else { trackingDeviceSource->StartTracking(); } } } mitk::NavigationDataSource::Pointer mitk::USCombinedModality::GetNavigationDataSource() { return m_LastFilter.GetPointer(); } bool mitk::USCombinedModality::GetIsCalibratedForCurrentStatus() { return m_Calibrations.find(this->GetIdentifierForCurrentCalibration()) != m_Calibrations.end(); } bool mitk::USCombinedModality::GetContainsAtLeastOneCalibration() { return ! m_Calibrations.empty(); } void mitk::USCombinedModality::GenerateData() { - // update ultrasound image source and get current output then - //m_UltrasoundDevice->Modified(); - m_UltrasoundDevice->Update(); - mitk::Image::Pointer image = m_UltrasoundDevice->GetOutput(); - if ( image.IsNull() || ! image->IsInitialized() ) { - return; - } + //get next image from ultrasound image source + mitk::Image::Pointer image = m_UltrasoundDevice->GetUSImageSource()->GetNextImage(); + if ( image.IsNull() || ! image->IsInitialized() ) //check the image + { + MITK_WARN << "Invalid image in USCombinedModality, aborting!"; + return; + } - // get output and initialize it if it wasn't initialized before - + //get output and initialize it if it wasn't initialized before mitk::Image::Pointer output = this->GetOutput(); if ( ! output->IsInitialized() ) { output->Initialize(image); } + //now update image data mitk::ImageReadAccessor inputReadAccessor(image, image->GetSliceData(0,0,0)); output->SetSlice(inputReadAccessor.GetData()); //copy image data output->GetGeometry()->SetSpacing(image->GetGeometry()->GetSpacing()); //copy spacing because this might also change - + //and update calibration (= transformation of the image) std::string calibrationKey = this->GetIdentifierForCurrentCalibration(); if ( ! calibrationKey.empty() ) { std::map::iterator calibrationIterator = m_Calibrations.find(calibrationKey); if ( calibrationIterator != m_Calibrations.end()) { // transform image according to callibration if one is set // for current configuration of probe and depth this->GetOutput()->GetGeometry()->SetIndexToWorldTransform(calibrationIterator->second); } } } std::string mitk::USCombinedModality::SerializeCalibration() { std::stringstream result; result << "" << std::endl; // For each calibration in the set for (std::map::iterator it = m_Calibrations.begin(); it != m_Calibrations.end(); it++) { mitk::AffineTransform3D::MatrixType matrix = it->second->GetMatrix(); mitk::AffineTransform3D::TranslationType translation = it->second->GetTranslation(); TiXmlElement elem(it->first); // Serialize Matrix elem.SetDoubleAttribute("M00", matrix[0][0]); elem.SetDoubleAttribute("M01", matrix[0][1]); elem.SetDoubleAttribute("M02", matrix[0][2]); elem.SetDoubleAttribute("M10", matrix[1][0]); elem.SetDoubleAttribute("M11", matrix[1][1]); elem.SetDoubleAttribute("M12", matrix[1][2]); elem.SetDoubleAttribute("M20", matrix[2][0]); elem.SetDoubleAttribute("M21", matrix[2][1]); elem.SetDoubleAttribute("M22", matrix[2][2]); // Serialize Offset elem.SetDoubleAttribute("T0", translation[0]); elem.SetDoubleAttribute("T1", translation[1]); elem.SetDoubleAttribute("T2", translation[2]); result << elem << std::endl; } result << "" << std::endl; return result.str(); } void mitk::USCombinedModality::DeserializeCalibration(const std::string& xmlString, bool clearPreviousCalibrations) { // Sanitize Input if (xmlString == "") { MITK_ERROR << "Empty string passed to Deserialize() method of CombinedModality. Aborting..."; mitkThrow() << "Empty string passed to Deserialize() method of CombinedModality. Aborting..."; return; } // Clear previous calibrations if necessary if (clearPreviousCalibrations) m_Calibrations.clear(); // Parse Input TiXmlDocument doc; if(!doc.Parse(xmlString.c_str())) { MITK_ERROR << "Unable to deserialize calibrations in CombinedModality. Error was: " << doc.ErrorDesc(); mitkThrow() << "Unable to deserialize calibrations in CombinedModality. Error was: " << doc.ErrorDesc(); return; } TiXmlElement* root = doc.FirstChildElement(); if(root == NULL) { MITK_ERROR << "Unable to deserialize calibrations in CombinedModality. String contained no root element."; mitkThrow() << "Unable to deserialize calibrations in CombinedModality. String contained no root element."; return; } // Read Calibrations for(TiXmlElement* elem = root->FirstChildElement(); elem != NULL; elem = elem->NextSiblingElement()) { mitk::AffineTransform3D::MatrixType matrix; mitk::AffineTransform3D::OffsetType translation; std::string calibName = elem->Value(); // Deserialize Matrix elem->QueryDoubleAttribute("M00", &matrix[0][0]); elem->QueryDoubleAttribute("M01", &matrix[0][1]); elem->QueryDoubleAttribute("M02", &matrix[0][2]); elem->QueryDoubleAttribute("M10", &matrix[1][0]); elem->QueryDoubleAttribute("M11", &matrix[1][1]); elem->QueryDoubleAttribute("M12", &matrix[1][2]); elem->QueryDoubleAttribute("M20", &matrix[2][0]); elem->QueryDoubleAttribute("M21", &matrix[2][1]); elem->QueryDoubleAttribute("M22", &matrix[2][2]); // Deserialize Offset elem->QueryDoubleAttribute("T0", &translation[0]); elem->QueryDoubleAttribute("T1", &translation[1]); elem->QueryDoubleAttribute("T2", &translation[2]); mitk::AffineTransform3D::Pointer calibration = mitk::AffineTransform3D::New(); calibration->SetMatrix(matrix); calibration->SetTranslation(translation); m_Calibrations[calibName] = calibration; } } std::string mitk::USCombinedModality::GetIdentifierForCurrentCalibration() { return this->GetIdentifierForCurrentProbe() + mitk::USCombinedModality::ProbeAndDepthSeperator + this->GetCurrentDepthValue(); } std::string mitk::USCombinedModality::GetIdentifierForCurrentProbe() { us::ServiceProperties usdeviceProperties = m_UltrasoundDevice->GetServiceProperties(); us::ServiceProperties::const_iterator probeIt = usdeviceProperties.find( mitk::USCombinedModality::GetPropertyKeys().US_PROPKEY_PROBES_SELECTED); // get probe identifier from control interface for probes std::string probeName = mitk::USCombinedModality::DefaultProbeIdentifier; if (probeIt != usdeviceProperties.end()) { probeName = (probeIt->second).ToString(); } // make sure that there is no '/' which would cause problems for TinyXML std::replace(probeName.begin(), probeName.end(), '/', '-'); return probeName; } std::string mitk::USCombinedModality::GetCurrentDepthValue() { us::ServiceProperties usdeviceProperties = m_UltrasoundDevice->GetServiceProperties(); // get string for depth value from the micro service properties std::string depth; us::ServiceProperties::iterator depthIterator = usdeviceProperties.find( mitk::USCombinedModality::GetPropertyKeys().US_PROPKEY_BMODE_DEPTH); if (depthIterator != usdeviceProperties.end()) { depth = depthIterator->second.ToString(); } else { depth = "0"; } return depth; } void mitk::USCombinedModality::RebuildFilterPipeline() { m_LastFilter = m_TrackingDevice; if ( m_NumberOfSmoothingValues > 0 ) { for (unsigned int i = 0; i < m_TrackingDevice->GetNumberOfOutputs(); i++) { m_SmoothingFilter->SetInput(i, m_LastFilter->GetOutput(i)); } m_LastFilter = m_SmoothingFilter; } if ( m_DelayCount > 0 ) { for (unsigned int i = 0; i < m_TrackingDevice->GetNumberOfOutputs(); i++) { m_DelayFilter->SetInput(i, m_LastFilter->GetOutput(i)); } m_LastFilter = m_DelayFilter; } }