diff --git a/Modules/US/USNavigation/mitkAbstractUltrasoundTrackerDevice.cpp b/Modules/US/USNavigation/mitkAbstractUltrasoundTrackerDevice.cpp index 19e989ad48..f467d89616 100644 --- a/Modules/US/USNavigation/mitkAbstractUltrasoundTrackerDevice.cpp +++ b/Modules/US/USNavigation/mitkAbstractUltrasoundTrackerDevice.cpp @@ -1,474 +1,463 @@ /*=================================================================== 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 "mitkAbstractUltrasoundTrackerDevice.h" #include "mitkImageReadAccessor.h" -#include "mitkNavigationDataSmoothingFilter.h" #include "mitkNavigationDataDelayFilter.h" #include "mitkNavigationDataDisplacementFilter.h" +#include "mitkNavigationDataSmoothingFilter.h" #include "mitkTrackingDeviceSource.h" // US Control Interfaces -#include "mitkUSControlInterfaceProbes.h" #include "mitkUSControlInterfaceBMode.h" #include "mitkUSControlInterfaceDoppler.h" +#include "mitkUSControlInterfaceProbes.h" -//Microservices +// Microservices #include #include -#include #include +#include #include -//TempIncludes +// TempIncludes #include -const std::string mitk::AbstractUltrasoundTrackerDevice::DeviceClassIdentifier = "org.mitk.modules.us.AbstractUltrasoundTrackerDevice"; -const char* mitk::AbstractUltrasoundTrackerDevice::DefaultProbeIdentifier = "default"; -const char* mitk::AbstractUltrasoundTrackerDevice::ProbeAndDepthSeperator = "_"; +const std::string mitk::AbstractUltrasoundTrackerDevice::DeviceClassIdentifier = + "org.mitk.modules.us.AbstractUltrasoundTrackerDevice"; +const char *mitk::AbstractUltrasoundTrackerDevice::DefaultProbeIdentifier = "default"; +const char *mitk::AbstractUltrasoundTrackerDevice::ProbeAndDepthSeperator = "_"; -const std::string mitk::AbstractUltrasoundTrackerDevice::US_INTERFACE_NAME = "org.mitk.services.AbstractUltrasoundTrackerDevice"; +const std::string mitk::AbstractUltrasoundTrackerDevice::US_INTERFACE_NAME = + "org.mitk.services.AbstractUltrasoundTrackerDevice"; const std::string mitk::AbstractUltrasoundTrackerDevice::US_PROPKEY_DEVICENAME = US_INTERFACE_NAME + ".devicename"; const std::string mitk::AbstractUltrasoundTrackerDevice::US_PROPKEY_CLASS = US_INTERFACE_NAME + ".class"; const std::string mitk::AbstractUltrasoundTrackerDevice::US_PROPKEY_ID = US_INTERFACE_NAME + ".id"; //____ - -mitk::AbstractUltrasoundTrackerDevice::AbstractUltrasoundTrackerDevice( - USDevice::Pointer usDevice, NavigationDataSource::Pointer trackingDevice, - bool trackedUltrasoundActive ) : - m_UltrasoundDevice(usDevice), m_TrackingDeviceDataSource(trackingDevice), +mitk::AbstractUltrasoundTrackerDevice::AbstractUltrasoundTrackerDevice(USDevice::Pointer usDevice, + NavigationDataSource::Pointer trackingDevice, + bool trackedUltrasoundActive) + : m_UltrasoundDevice(usDevice), + m_TrackingDeviceDataSource(trackingDevice), m_SmoothingFilter(mitk::NavigationDataSmoothingFilter::New()), m_DelayFilter(mitk::NavigationDataDelayFilter::New(0)), m_DisplacementFilter(mitk::NavigationDataDisplacementFilter::New()), m_LastFilterOfIGTPipeline(nullptr), - m_NumberOfSmoothingValues(0), m_DelayCount(0), - m_IsTrackedUltrasoundActive( trackedUltrasoundActive ) + m_NumberOfSmoothingValues(0), + m_DelayCount(0), + m_IsTrackedUltrasoundActive(trackedUltrasoundActive) { m_DisplacementFilter->SetTransform6DOF(true); this->RebuildFilterPipeline(); - //create a new output (for the image data) + // 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 //___ m_UltrasoundDevice->SetSpawnAcquireThread(false); } +mitk::AffineTransform3D::Pointer mitk::AbstractUltrasoundTrackerDevice::GetUSPlaneTransform() +{ + return mitk::AffineTransform3D::New(); +} mitk::AbstractUltrasoundTrackerDevice::~AbstractUltrasoundTrackerDevice() { if (m_ServiceRegistration != nullptr) { m_ServiceRegistration.Unregister(); } m_ServiceRegistration = 0; } -mitk::AffineTransform3D::Pointer - mitk::AbstractUltrasoundTrackerDevice::GetCalibration() +mitk::AffineTransform3D::Pointer mitk::AbstractUltrasoundTrackerDevice::GetCalibration() { - return this->GetCalibration( this->GetCurrentDepthValue(), - this->GetIdentifierForCurrentProbe() ); + return this->GetCalibration(this->GetCurrentDepthValue(), this->GetIdentifierForCurrentProbe()); } -mitk::AffineTransform3D::Pointer - mitk::AbstractUltrasoundTrackerDevice::GetCalibration(std::string depth) +mitk::AffineTransform3D::Pointer mitk::AbstractUltrasoundTrackerDevice::GetCalibration(std::string depth) { return this->GetCalibration(depth, this->GetIdentifierForCurrentProbe()); } -mitk::AffineTransform3D::Pointer - mitk::AbstractUltrasoundTrackerDevice::GetCalibration( std::string depth, - std::string probe ) +mitk::AffineTransform3D::Pointer mitk::AbstractUltrasoundTrackerDevice::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::AbstractUltrasoundTrackerDevice::ProbeAndDepthSeperator + - depth; + std::string calibrationKey = probe + mitk::AbstractUltrasoundTrackerDevice::ProbeAndDepthSeperator + depth; // find calibration for combination of probe identifier and depth - std::map::iterator calibrationIterator - = m_Calibrations.find(calibrationKey); + std::map::iterator calibrationIterator = + m_Calibrations.find(calibrationKey); - if (calibrationIterator == m_Calibrations.end()) { return 0; } + if (calibrationIterator == m_Calibrations.end()) + { + return 0; + } return calibrationIterator->second; } -void mitk::AbstractUltrasoundTrackerDevice::SetCalibration( - mitk::AffineTransform3D::Pointer calibration ) +void mitk::AbstractUltrasoundTrackerDevice::SetCalibration(mitk::AffineTransform3D::Pointer calibration) { - if( calibration.IsNull() ) + if (calibration.IsNull()) { MITK_WARN << "Null pointer passed to SetCalibration of mitk::USDevice. Ignoring call."; return; } std::string calibrationKey = this->GetIdentifierForCurrentCalibration(); - if( calibrationKey.empty() ) + if (calibrationKey.empty()) { MITK_WARN << "Could not get a key for the calibration -> Calibration cannot be set."; return; } m_Calibrations[calibrationKey] = calibration; } bool mitk::AbstractUltrasoundTrackerDevice::RemoveCalibration() { - return this->RemoveCalibration( this->GetCurrentDepthValue(), - this->GetIdentifierForCurrentProbe() ); + return this->RemoveCalibration(this->GetCurrentDepthValue(), this->GetIdentifierForCurrentProbe()); } bool mitk::AbstractUltrasoundTrackerDevice::RemoveCalibration(std::string depth) { - return this->RemoveCalibration( depth, - this->GetIdentifierForCurrentProbe() ); + return this->RemoveCalibration(depth, this->GetIdentifierForCurrentProbe()); } -bool mitk::AbstractUltrasoundTrackerDevice::RemoveCalibration( std::string depth, - std::string probe ) +bool mitk::AbstractUltrasoundTrackerDevice::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::AbstractUltrasoundTrackerDevice::ProbeAndDepthSeperator + - depth; + std::string calibrationKey = probe + mitk::AbstractUltrasoundTrackerDevice::ProbeAndDepthSeperator + depth; return m_Calibrations.erase(calibrationKey) > 0; } std::string mitk::AbstractUltrasoundTrackerDevice::GetDeviceClass() { return DeviceClassIdentifier; } mitk::USImageSource::Pointer mitk::AbstractUltrasoundTrackerDevice::GetUSImageSource() { if (m_UltrasoundDevice.IsNull()) { MITK_ERROR("AbstractUltrasoundTrackerDevice")("USDevice") << "UltrasoundDevice must not be null."; mitkThrow() << "UltrasoundDevice must not be null."; } return m_UltrasoundDevice->GetUSImageSource(); } mitk::NavigationDataSource::Pointer mitk::AbstractUltrasoundTrackerDevice::GetNavigationDataSource() { - if( m_LastFilterOfIGTPipeline.IsNull() ) + if (m_LastFilterOfIGTPipeline.IsNull()) { this->RebuildFilterPipeline(); } m_LastFilterOfIGTPipeline->SetToolMetaDataCollection(this->m_TrackingDeviceDataSource->GetToolMetaDataCollection()); return m_LastFilterOfIGTPipeline; } bool mitk::AbstractUltrasoundTrackerDevice::GetIsCalibratedForCurrentStatus() { return m_Calibrations.find(this->GetIdentifierForCurrentCalibration()) != m_Calibrations.end(); } bool mitk::AbstractUltrasoundTrackerDevice::GetContainsAtLeastOneCalibration() { return !m_Calibrations.empty(); } std::string mitk::AbstractUltrasoundTrackerDevice::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++ ) + 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::AbstractUltrasoundTrackerDevice::DeserializeCalibration( - const std::string& xmlString, - bool clearPreviousCalibrations ) +void mitk::AbstractUltrasoundTrackerDevice::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(); + 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(); + TiXmlElement *root = doc.FirstChildElement(); if (root == nullptr) { 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 != nullptr; elem = elem->NextSiblingElement()) + for (TiXmlElement *elem = root->FirstChildElement(); elem != nullptr; 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; } } -void mitk::AbstractUltrasoundTrackerDevice::SetNumberOfSmoothingValues( - unsigned int numberOfSmoothingValues ) +void mitk::AbstractUltrasoundTrackerDevice::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)) + if ((oldNumber == 0 && numberOfSmoothingValues != 0) || (oldNumber != 0 && numberOfSmoothingValues == 0)) { this->RebuildFilterPipeline(); } m_SmoothingFilter->SetNumerOfValues(numberOfSmoothingValues); } -void mitk::AbstractUltrasoundTrackerDevice::SetDelayCount( unsigned int delayCount ) +void mitk::AbstractUltrasoundTrackerDevice::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)) + if ((oldCount == 0 && delayCount != 0) || (oldCount != 0 && delayCount == 0)) { this->RebuildFilterPipeline(); } m_DelayFilter->SetDelay(delayCount); } -void mitk::AbstractUltrasoundTrackerDevice::GenerateData() -{ -} +void mitk::AbstractUltrasoundTrackerDevice::GenerateData() {} std::string mitk::AbstractUltrasoundTrackerDevice::GetIdentifierForCurrentCalibration() { - return this->GetIdentifierForCurrentProbe() - + mitk::AbstractUltrasoundTrackerDevice::ProbeAndDepthSeperator - + this->GetCurrentDepthValue(); + return this->GetIdentifierForCurrentProbe() + mitk::AbstractUltrasoundTrackerDevice::ProbeAndDepthSeperator + + this->GetCurrentDepthValue(); } std::string mitk::AbstractUltrasoundTrackerDevice::GetIdentifierForCurrentProbe() { us::ServiceProperties usdeviceProperties = m_UltrasoundDevice->GetServiceProperties(); - us::ServiceProperties::const_iterator probeIt = usdeviceProperties.find( - mitk::USDevice::GetPropertyKeys().US_PROPKEY_PROBES_SELECTED); + us::ServiceProperties::const_iterator probeIt = + usdeviceProperties.find(mitk::USDevice::GetPropertyKeys().US_PROPKEY_PROBES_SELECTED); // get probe identifier from control interface for probes std::string probeName = mitk::AbstractUltrasoundTrackerDevice::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::AbstractUltrasoundTrackerDevice::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::USDevice::GetPropertyKeys().US_PROPKEY_BMODE_DEPTH); + us::ServiceProperties::iterator depthIterator = + usdeviceProperties.find(mitk::USDevice::GetPropertyKeys().US_PROPKEY_BMODE_DEPTH); if (depthIterator != usdeviceProperties.end()) { depth = depthIterator->second.ToString(); } else { depth = "0"; } return depth; } void mitk::AbstractUltrasoundTrackerDevice::RebuildFilterPipeline() { m_LastFilterOfIGTPipeline = m_TrackingDeviceDataSource; - if( m_NumberOfSmoothingValues > 0 ) + if (m_NumberOfSmoothingValues > 0) { m_SmoothingFilter->ConnectTo(m_LastFilterOfIGTPipeline.GetPointer()); m_LastFilterOfIGTPipeline = m_SmoothingFilter; } - if( m_DelayCount > 0 ) + if (m_DelayCount > 0) { m_DelayFilter->ConnectTo(m_LastFilterOfIGTPipeline.GetPointer()); m_LastFilterOfIGTPipeline = m_DelayFilter; } - if( m_IsTrackedUltrasoundActive ) + if (m_IsTrackedUltrasoundActive) { m_DisplacementFilter->ConnectTo(m_LastFilterOfIGTPipeline.GetPointer()); m_LastFilterOfIGTPipeline = m_DisplacementFilter; } } void mitk::AbstractUltrasoundTrackerDevice::UnregisterOnService() { if (m_UltrasoundDevice->GetDeviceState() == USDevice::State_Activated) { m_UltrasoundDevice->Deactivate(); } if (m_UltrasoundDevice->GetDeviceState() == USDevice::State_Connected) { m_UltrasoundDevice->Disconnect(); } if (m_ServiceRegistration != nullptr) m_ServiceRegistration.Unregister(); m_ServiceRegistration = 0; } void mitk::AbstractUltrasoundTrackerDevice::RegisterAsMicroservice() { - //Get Context - us::ModuleContext* context = us::GetModuleContext(); + // Get Context + us::ModuleContext *context = us::GetModuleContext(); - //Define ServiceProps - //us::ServiceProperties props; - mitk::UIDGenerator uidGen = - mitk::UIDGenerator("org.mitk.services.AbstractUltrasoundTrackerDevice", 16); + // Define ServiceProps + // us::ServiceProperties props; + mitk::UIDGenerator uidGen = mitk::UIDGenerator("org.mitk.services.AbstractUltrasoundTrackerDevice", 16); m_ServiceProperties[US_PROPKEY_ID] = uidGen.GetUID(); m_ServiceProperties[US_PROPKEY_DEVICENAME] = m_UltrasoundDevice->GetName(); m_ServiceProperties[US_PROPKEY_CLASS] = mitk::AbstractUltrasoundTrackerDevice::DeviceClassIdentifier; m_ServiceRegistration = context->RegisterService(this, m_ServiceProperties); } mitk::USAbstractControlInterface::Pointer mitk::AbstractUltrasoundTrackerDevice::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::AbstractUltrasoundTrackerDevice::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::AbstractUltrasoundTrackerDevice::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::AbstractUltrasoundTrackerDevice::GetControlInterfaceDoppler() { if (m_UltrasoundDevice.IsNull()) { MITK_ERROR("USCombinedModality")("USDevice") << "UltrasoundDevice must not be null."; mitkThrow() << "UltrasoundDevice must not be null."; } return m_UltrasoundDevice->GetControlInterfaceDoppler(); } diff --git a/Modules/US/USNavigation/mitkAbstractUltrasoundTrackerDevice.h b/Modules/US/USNavigation/mitkAbstractUltrasoundTrackerDevice.h index 8e0f8bf705..03eb9b8728 100644 --- a/Modules/US/USNavigation/mitkAbstractUltrasoundTrackerDevice.h +++ b/Modules/US/USNavigation/mitkAbstractUltrasoundTrackerDevice.h @@ -1,257 +1,260 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef __mitkAbstractUltrasoundTrackerDevice_h #define __mitkAbstractUltrasoundTrackerDevice_h #include #include "mitkUSDevice.h" #include "mitkImageSource.h" #include "mitkNavigationDataSource.h" // Microservices #include #include #include #include #include #include namespace itk { template class SmartPointer; } namespace mitk { class NavigationDataSmoothingFilter; class NavigationDataDelayFilter; class NavigationDataDisplacementFilter; /** * \brief Abstract class for an easy handling of a combination of an USDevice and * a NavigationDataSource. * This class can be used as an ImageSource subclass. Additionally tracking data be * retrieved from the NavigationDataSource returned by GetTrackingDevice(). * * A calibration of the ultrasound image stream to the navigation datas can be set * for the currently active zoom level (of the ultrasound device) by SetCalibration() * The ultrasound images are transformed according to this calibration in the * GenerateData() method. */ class MITKUSNAVIGATION_EXPORT AbstractUltrasoundTrackerDevice : public mitk::ImageSource { public: static const std::string DeviceClassIdentifier; static const char* DefaultProbeIdentifier; static const char* ProbeAndDepthSeperator; static const std::string US_INTERFACE_NAME; static const std::string US_PROPKEY_DEVICENAME; static const std::string US_PROPKEY_CLASS; static const std::string US_PROPKEY_ID; mitkClassMacro(AbstractUltrasoundTrackerDevice, mitk::ImageSource); mitkNewMacro3Param(AbstractUltrasoundTrackerDevice, USDevice::Pointer, itk::SmartPointer, bool); itkGetMacro(UltrasoundDevice, itk::SmartPointer); itkSetMacro(UltrasoundDevice, itk::SmartPointer); itkGetMacro(TrackingDeviceDataSource, itk::SmartPointer); itkSetMacro(TrackingDeviceDataSource, itk::SmartPointer); itkGetMacro(IsTrackedUltrasoundActive, bool); /** * \brief Getter for calibration data of the currently active depth and probe. * * \return Transformation for calibration or null if no calibration is available. */ AffineTransform3D::Pointer GetCalibration(); /** * \brief Getter for calibration data of the given depth and the currently active probe. * * \param depth depth of the b mode ultrasound image for which the calibration should be returned * \return Transformation for calibration or null if no calibration is available. */ AffineTransform3D::Pointer GetCalibration(std::string depth); /** * \brief Getter for calibration data of the given depth and probe. * * \param depth depth of the b mode ultrasound image for which the calibration should be returned * \param probe probe of the ultrasound device for which the calibration should be returned * \return Transformation for calibration or null if no calibration is available. */ AffineTransform3D::Pointer GetCalibration(std::string depth, std::string probe); + /** Returns the index to world transform of the US plane. */ + virtual AffineTransform3D::Pointer GetUSPlaneTransform(); + /** * \brief Sets a transformation as calibration data. * Calibration data is set for the currently activated probe and their current * zoom factor. It also marks the device as calibrated. */ void SetCalibration(AffineTransform3D::Pointer calibration); /** * \brief Removes the calibration data of the currently active depth and probe. * \return true on success, false if there was no calibration */ bool RemoveCalibration(); /** * \brief Removes the calibration data of the given depth and the currently active probe. * * \param depth depth of the b mode ultrasound image for which the calibration should be removed * \return true on success, false if there was no calibration */ bool RemoveCalibration(std::string depth); /** * \brief Removes the calibration data of the given depth and probe. * * \param depth depth of the b mode ultrasound image for which the calibration should be removed * \param probe probe of the ultrasound device for which the calibration should be removed * \return true on success, false if there was no calibration */ bool RemoveCalibration(std::string depth, std::string probe); /** * \brief Returns the Class of the Device. */ std::string GetDeviceClass(); /** * \brief Wrapper for returning USImageSource of the UltrasoundDevice. */ USImageSource::Pointer GetUSImageSource(); itk::SmartPointer GetNavigationDataSource(); /** * \return true if the device is calibrated for the currently selected probe with the current zoom level */ bool GetIsCalibratedForCurrentStatus(); /** * \return true if a calibration was loaded for at least one probe and depth */ bool GetContainsAtLeastOneCalibration(); /** * \brief Serializes all contained calibrations into an xml fragment. * * The returned string contains one parent node named "calibrations" and several * subnodes, one for each calibration that is present. */ std::string SerializeCalibration(); /** * \brief Deserializes a string provided by a prior call to Serialize(). * If the bool flag is true, all prior calibrations will be deleted. * If the flag is set to false, prior calibrations will be retained, but overwritten * if one of equal name is present. * * \throws mitk::Exception if the given string could not be parsed correctly. */ void DeserializeCalibration(const std::string &xmlString, bool clearPreviousCalibrations = true); void SetNumberOfSmoothingValues(unsigned int numberOfSmoothingValues); void SetDelayCount(unsigned int delayCount); /** * \brief Remove this device from the micro service. * This method is public for mitk::USCombinedModality, because this devices * can be completly removed. This is not possible for API devices, which * should be available while their sub module is loaded. */ void UnregisterOnService(); virtual void RegisterAsMicroservice(); /** * \brief Wrapper for returning custom control interface of the UltrasoundDevice. */ virtual itk::SmartPointer GetControlInterfaceCustom(); /** * \brief Wrapper for returning B mode control interface of the UltrasoundDevice. */ virtual itk::SmartPointer GetControlInterfaceBMode(); /** * \brief Wrapper for returning probes control interface of the UltrasoundDevice. */ virtual itk::SmartPointer GetControlInterfaceProbes(); /** * \brief Wrapper for returning doppler control interface of the UltrasoundDevice. */ virtual itk::SmartPointer GetControlInterfaceDoppler(); protected: AbstractUltrasoundTrackerDevice( USDevice::Pointer usDevice, itk::SmartPointer trackingDevice, bool trackedUltrasoundActive ); virtual ~AbstractUltrasoundTrackerDevice(); /** * \brief Grabs the next frame from the input. * Must be implemented by the derived class. * This method is called internally, whenever Update() is invoked by an Output. */ virtual void GenerateData() override; std::string GetIdentifierForCurrentCalibration(); std::string GetIdentifierForCurrentProbe(); std::string GetCurrentDepthValue(); void RebuildFilterPipeline(); USDevice::Pointer m_UltrasoundDevice; itk::SmartPointer m_TrackingDeviceDataSource; std::map m_Calibrations; itk::SmartPointer m_SmoothingFilter; itk::SmartPointer m_DelayFilter; itk::SmartPointer m_DisplacementFilter; itk::SmartPointer m_LastFilterOfIGTPipeline; unsigned int m_NumberOfSmoothingValues; unsigned int m_DelayCount; /** * \brief The device's ServiceRegistration object that allows to modify it's Microservice registraton details. */ us::ServiceRegistration m_ServiceRegistration; /** * \brief Properties of the device's Microservice. */ us::ServiceProperties m_ServiceProperties; private: bool m_IsTrackedUltrasoundActive; }; } // namespace mitk MITK_DECLARE_SERVICE_INTERFACE(mitk::AbstractUltrasoundTrackerDevice, "org.mitk.services.AbstractUltrasoundTrackerDevice") #endif diff --git a/Modules/US/USNavigation/mitkTrackedUltrasound.cpp b/Modules/US/USNavigation/mitkTrackedUltrasound.cpp index 774b3d9150..d8abef4d52 100644 --- a/Modules/US/USNavigation/mitkTrackedUltrasound.cpp +++ b/Modules/US/USNavigation/mitkTrackedUltrasound.cpp @@ -1,79 +1,84 @@ /*=================================================================== 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 "mitkTrackedUltrasound.h" #include "mitkImageReadAccessor.h" #include #include #include "mitkNavigationDataDisplacementFilter.h" #include "mitkTrackingDeviceSource.h" mitk::TrackedUltrasound::TrackedUltrasound( USDevice::Pointer usDevice, NavigationDataSource::Pointer trackingDevice, bool trackedUltrasoundActive ) : AbstractUltrasoundTrackerDevice( usDevice, trackingDevice, trackedUltrasoundActive ) { } mitk::TrackedUltrasound::~TrackedUltrasound() { } +mitk::AffineTransform3D::Pointer mitk::TrackedUltrasound::GetUSPlaneTransform() +{ + return m_UltrasoundDevice->GetOutput(0)->GetGeometry()->GetIndexToWorldTransform(); +} + void mitk::TrackedUltrasound::GenerateData() { //Call Update auf US-Device + evtl. auf Tracker (???) if (m_UltrasoundDevice->GetIsFreezed()) { return; } //if the image is freezed: do nothing //get next image from ultrasound image source //FOR LATER: Be aware if the for loop behaves correct, if the UltrasoundDevice has more than 1 output. int i = 0; m_UltrasoundDevice->Update(); mitk::Image::Pointer image = m_UltrasoundDevice->GetOutput(i); if (image.IsNull() || !image->IsInitialized()) //check the image { MITK_WARN << "Invalid image in TrackedUltrasound, aborting!"; return; } //___MITK_INFO << "GetSpacing: " << image->GetGeometry()->GetSpacing(); //get output and initialize it if it wasn't initialized before mitk::Image::Pointer output = this->GetOutput(i); 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 m_DisplacementFilter->SetTransformation(calibrationIterator->second); //Setze Update auf Displacementfilter ???? } } } diff --git a/Modules/US/USNavigation/mitkTrackedUltrasound.h b/Modules/US/USNavigation/mitkTrackedUltrasound.h index e05f650bd5..6395e63cb0 100644 --- a/Modules/US/USNavigation/mitkTrackedUltrasound.h +++ b/Modules/US/USNavigation/mitkTrackedUltrasound.h @@ -1,66 +1,67 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef __mitkTrackedUltrasound_h #define __mitkTrackedUltrasound_h #include #include "mitkUSDevice.h" #include "mitkImageSource.h" #include "mitkAbstractUltrasoundTrackerDevice.h" #include "mitkNavigationDataSource.h" namespace itk { template class SmartPointer; } namespace mitk { /** * \brief Combination of USDevice and NavigationDataSource. * This class can be used as an ImageSource subclass. Additionally tracking data be * retrieved from the NavigationDataSource returned by GetTrackingDevice(). * * A calibration of the ultrasound image stream to the navigation datas can be set * for the currently active zoom level (of the ultrasound device) by SetCalibration(). * The ultrasound images are transformed according to this calibration in the * GenerateData() method. */ class MITKUSNAVIGATION_EXPORT TrackedUltrasound : public mitk::AbstractUltrasoundTrackerDevice { public: mitkClassMacro(TrackedUltrasound, mitk::AbstractUltrasoundTrackerDevice); mitkNewMacro3Param(TrackedUltrasound, USDevice::Pointer, itk::SmartPointer, bool); + virtual AffineTransform3D::Pointer GetUSPlaneTransform(); protected: TrackedUltrasound( USDevice::Pointer usDevice, itk::SmartPointer trackingDevice, bool trackedUltrasoundActive = true ); virtual ~TrackedUltrasound(); /** * \brief Grabs the next frame from the input. * This method is called internally, whenever Update() is invoked by an Output. */ void GenerateData() override; }; } // namespace mitk #endif // __mitkTrackedUltrasound_h diff --git a/Modules/US/USNavigation/mitkUSCombinedModality.cpp b/Modules/US/USNavigation/mitkUSCombinedModality.cpp index b7c23d1470..4c9a33053c 100644 --- a/Modules/US/USNavigation/mitkUSCombinedModality.cpp +++ b/Modules/US/USNavigation/mitkUSCombinedModality.cpp @@ -1,77 +1,84 @@ /*=================================================================== 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 "mitkImageReadAccessor.h" -#include -#include #include "mitkTrackingDeviceSource.h" +#include "mitkUSCombinedModality.h" +#include +#include // US Control Interfaces -#include "mitkUSControlInterfaceProbes.h" #include "mitkUSControlInterfaceBMode.h" #include "mitkUSControlInterfaceDoppler.h" +#include "mitkUSControlInterfaceProbes.h" -mitk::USCombinedModality::USCombinedModality( USDevice::Pointer usDevice, - NavigationDataSource::Pointer trackingDevice, - bool trackedUltrasoundActive ) - : AbstractUltrasoundTrackerDevice( usDevice, trackingDevice, trackedUltrasoundActive ) +mitk::USCombinedModality::USCombinedModality(USDevice::Pointer usDevice, + NavigationDataSource::Pointer trackingDevice, + bool trackedUltrasoundActive) + : AbstractUltrasoundTrackerDevice(usDevice, trackingDevice, trackedUltrasoundActive) { } - -mitk::USCombinedModality::~USCombinedModality() +mitk::AffineTransform3D::Pointer mitk::USCombinedModality::GetUSPlaneTransform() { + return this->GetCalibration(); } +mitk::USCombinedModality::~USCombinedModality() {} void mitk::USCombinedModality::GenerateData() { - if (m_UltrasoundDevice->GetIsFreezed()) { return; } //if the image is freezed: do nothing - - //get next image from ultrasound image source - //FOR LATER: Be aware if the for loop behaves correct, if the UltrasoundDevice has more than 1 output. + if (m_UltrasoundDevice->GetIsFreezed()) + { + return; + } // if the image is freezed: do nothing + + // get next image from ultrasound image source + // FOR LATER: Be aware if the for loop behaves correct, if the UltrasoundDevice has more than 1 output. int i = 0; m_UltrasoundDevice->Update(); mitk::Image::Pointer image = m_UltrasoundDevice->GetOutput(0); - if (image.IsNull() || !image->IsInitialized()) //check the image + 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); } + if (!output->IsInitialized()) + { + output->Initialize(image); + } - //now update image data + // 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 + 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) + // and update calibration (= transformation of the image) std::string calibrationKey = this->GetIdentifierForCurrentCalibration(); if (!calibrationKey.empty()) { - std::map::iterator calibrationIterator - = m_Calibrations.find(calibrationKey); + 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); } } } diff --git a/Modules/US/USNavigation/mitkUSCombinedModality.h b/Modules/US/USNavigation/mitkUSCombinedModality.h index d9f5c3ae62..60963adcaf 100644 --- a/Modules/US/USNavigation/mitkUSCombinedModality.h +++ b/Modules/US/USNavigation/mitkUSCombinedModality.h @@ -1,71 +1,72 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef MITKUSCombinedModality_H_HEADER_INCLUDED_ #define MITKUSCombinedModality_H_HEADER_INCLUDED_ #include #include "mitkUSDevice.h" #include "mitkImageSource.h" #include "mitkAbstractUltrasoundTrackerDevice.h" #include "mitkNavigationDataSource.h" // Microservices #include #include namespace itk { template class SmartPointer; } namespace mitk { class USControlInterfaceBMode; class USControlInterfaceProbes; class USControlInterfaceDoppler; /** * \brief Combination of USDevice and NavigationDataSource. * This class can be used as an ImageSource subclass. Additionally tracking data be * retrieved from the NavigationDataSource returned by GetTrackingDevice(). * * A calibration of the ultrasound image stream to the navigation datas can be set * for the currently active zoom level (of the ultrasound device) by SetCalibration(). * The ultrasound images are transformed according to this calibration in the * GenerateData() method. */ class MITKUSNAVIGATION_EXPORT USCombinedModality : public mitk::AbstractUltrasoundTrackerDevice { public: mitkClassMacro(USCombinedModality, mitk::AbstractUltrasoundTrackerDevice); mitkNewMacro3Param(USCombinedModality, USDevice::Pointer, itk::SmartPointer, bool); + virtual AffineTransform3D::Pointer GetUSPlaneTransform(); protected: USCombinedModality( USDevice::Pointer usDevice, itk::SmartPointer trackingDevice, bool trackedUltrasoundActive = false ); virtual ~USCombinedModality(); /** * \brief Grabs the next frame from the input. * This method is called internally, whenever Update() is invoked by an Output. */ void GenerateData() override; }; } // namespace mitk #endif // MITKUSCombinedModality_H_HEADER_INCLUDED_ diff --git a/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/NavigationStepWidgets/QmitkUSNavigationStepPunctuationIntervention.cpp b/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/NavigationStepWidgets/QmitkUSNavigationStepPunctuationIntervention.cpp index 4cc5291594..86635094b7 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/NavigationStepWidgets/QmitkUSNavigationStepPunctuationIntervention.cpp +++ b/Plugins/org.mitk.gui.qt.igt.app.echotrack/src/internal/NavigationStepWidgets/QmitkUSNavigationStepPunctuationIntervention.cpp @@ -1,294 +1,294 @@ /*=================================================================== 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 "QmitkUSNavigationStepPunctuationIntervention.h" #include "ui_QmitkUSNavigationStepPunctuationIntervention.h" #include "mitkNeedleProjectionFilter.h" #include "../Widgets/QmitkZoneProgressBar.h" #include "../QmitkUSNavigationMarkerPlacement.h" #include "usModuleRegistry.h" #include QmitkUSNavigationStepPunctuationIntervention::QmitkUSNavigationStepPunctuationIntervention(QWidget *parent) : QmitkUSAbstractNavigationStep(parent), m_Ui(new Ui::QmitkUSNavigationStepPunctuationIntervention), m_ZoneNodes(nullptr), m_NeedleProjectionFilter(mitk::NeedleProjectionFilter::New()), m_NeedleNavigationTool(mitk::NavigationTool::New()), m_OldColors(), m_SphereSource(vtkSmartPointer::New()), m_OBBTree(vtkSmartPointer::New()), m_IntersectPoints(vtkSmartPointer::New()) { m_Ui->setupUi(this); connect(m_Ui->m_AddNewAblationZone, SIGNAL(clicked()), this, SLOT(OnAddAblationZoneClicked())); connect(m_Ui->m_ShowToolAxisN, SIGNAL(stateChanged(int)), this, SLOT(OnShowToolAxisEnabled(int))); connect(m_Ui->m_EnableAblationMarking, SIGNAL(clicked()), this, SLOT(OnEnableAblationZoneMarkingClicked())); connect(m_Ui->m_AblationZoneSizeSlider, SIGNAL(valueChanged(int)), this, SLOT(OnAblationZoneSizeSliderChanged(int))); m_Ui->m_AblationZonesBox->setVisible(false); } void QmitkUSNavigationStepPunctuationIntervention::SetNeedleMetaData(mitk::NavigationTool::Pointer needleNavigationTool) { this->m_NeedleNavigationTool = needleNavigationTool; } void QmitkUSNavigationStepPunctuationIntervention::OnEnableAblationZoneMarkingClicked() { if(m_Ui->m_EnableAblationMarking->isChecked()) m_Ui->m_AblationZonesBox->setVisible(true); else m_Ui->m_AblationZonesBox->setVisible(false); } void QmitkUSNavigationStepPunctuationIntervention::OnAblationZoneSizeSliderChanged(int size) { int id = m_Ui->m_AblationZonesList->currentRow(); if (id!=-1) {emit AblationZoneChanged(id,size);} }// void QmitkUSNavigationStepPunctuationIntervention::OnAddAblationZoneClicked() { QListWidgetItem* newItem = new QListWidgetItem("Ablation Zone (initial size: " + QString::number(m_Ui->m_AblationZoneSizeSlider->value()) + " mm)", m_Ui->m_AblationZonesList); newItem->setSelected(true); emit AddAblationZoneClicked(m_Ui->m_AblationZoneSizeSlider->value()); } QmitkUSNavigationStepPunctuationIntervention::~QmitkUSNavigationStepPunctuationIntervention() { mitk::DataStorage::Pointer dataStorage = this->GetDataStorage(false); if ( dataStorage.IsNotNull() ) { // remove needle path from data storage if it is there mitk::DataNode::Pointer node = this->GetNamedDerivedNode ("Needle Path", QmitkUSAbstractNavigationStep::DATANAME_BASENODE); if ( node.IsNotNull() ) { dataStorage->Remove(node); } } delete m_Ui; } bool QmitkUSNavigationStepPunctuationIntervention::OnStartStep() { // create node for Needle Projection mitk::DataNode::Pointer node = this->GetNamedDerivedNodeAndCreate ("Needle Path", QmitkUSAbstractNavigationStep::DATANAME_BASENODE); node->SetData(m_NeedleProjectionFilter->GetProjection()); node->SetBoolProperty("show contour", true); - m_NeedleProjectionFilter->SetToolAxisForFilter(m_NeedleNavigationTool->GetToolAxis()); + //m_NeedleProjectionFilter->SetToolAxisForFilter(m_NeedleNavigationTool->GetToolAxis()); return true; } bool QmitkUSNavigationStepPunctuationIntervention::OnRestartStep() { return this->OnActivateStep(); } bool QmitkUSNavigationStepPunctuationIntervention::OnFinishStep() { mitk::DataNode::Pointer finishPunctionResult = mitk::DataNode::New(); finishPunctionResult->SetName("PunctionResult"); mitk::Point3D needlePos = m_NeedleProjectionFilter->GetOutput(0)->GetPosition(); mitk::Quaternion needleRot = m_NeedleProjectionFilter->GetOutput(0)->GetOrientation(); finishPunctionResult->SetProperty("USNavigation::TipPositionEnd", mitk::Point3dProperty::New(needlePos)); MITK_INFO("USNavigationLogging") << "Instrument tip at end: " <ClearZones(); mitk::DataStorage::Pointer dataStorage = this->GetDataStorage(); // add progress bars for risk zone nodes m_ZoneNodes = dataStorage->GetDerivations(dataStorage->GetNamedNode(QmitkUSNavigationMarkerPlacement::DATANAME_ZONES)); // add zones to the widgets for risk structures for (mitk::DataStorage::SetOfObjects::ConstIterator it = m_ZoneNodes->Begin(); it != m_ZoneNodes->End(); ++it) { m_Ui->riskStructuresRangeWidget->AddZone(it->Value()); float rgb[3]; it->Value()->GetColor(rgb); mitk::Color color; color.SetRed(rgb[0]); color.SetGreen(rgb[1]); color.SetBlue(rgb[2]); m_OldColors[it->Value()] = color; } m_NeedleProjectionFilter->SelectInput(0); return true; } void QmitkUSNavigationStepPunctuationIntervention::OnShowToolAxisEnabled(int enabled) { if (enabled == 0) { m_NeedleProjectionFilter->ShowToolAxis(false); } else { m_NeedleProjectionFilter->ShowToolAxis(true); } } void QmitkUSNavigationStepPunctuationIntervention::OnUpdate() { if (this->GetCombinedModality(false).IsNull()) return; // get navigation data source and make sure that it is not null mitk::NavigationDataSource::Pointer navigationDataSource = this->GetCombinedModality()->GetNavigationDataSource(); if ( navigationDataSource.IsNull() ) { MITK_ERROR("QmitkUSAbstractNavigationStep")("QmitkUSNavigationStepPunctuationIntervention") << "Navigation Data Source of Combined Modality must not be null."; mitkThrow() << "Navigation Data Source of Combined Modality must not be null."; } // update body marker this->UpdateBodyMarkerStatus(navigationDataSource->GetOutput(1)); // update critical structures this->UpdateCriticalStructures(navigationDataSource->GetOutput(0),m_NeedleProjectionFilter->GetProjection()); m_NeedleProjectionFilter->Update(); //Update Distance to US image mitk::Point3D point1 = m_NeedleProjectionFilter->GetProjection()->GetPoint(0); mitk::Point3D point2 = m_NeedleProjectionFilter->GetProjection()->GetPoint(1); double distance = point1.EuclideanDistanceTo(point2); m_Ui->m_DistanceToUSPlane->setText(QString::number(distance) + " mm"); } void QmitkUSNavigationStepPunctuationIntervention::OnSettingsChanged(const itk::SmartPointer settingsNode) { if ( settingsNode.IsNull() ) { return; } } QString QmitkUSNavigationStepPunctuationIntervention::GetTitle() { return "Computer-assisted Intervention"; } bool QmitkUSNavigationStepPunctuationIntervention::GetIsRestartable() { return false; } QmitkUSNavigationStepPunctuationIntervention::FilterVector QmitkUSNavigationStepPunctuationIntervention::GetFilter() { return FilterVector(1, m_NeedleProjectionFilter.GetPointer()); } void QmitkUSNavigationStepPunctuationIntervention::OnSetCombinedModality() { mitk::AbstractUltrasoundTrackerDevice::Pointer combinedModality = this->GetCombinedModality(false); if ( combinedModality.IsNotNull() ) { m_NeedleProjectionFilter->ConnectTo(combinedModality->GetNavigationDataSource()); // set calibration of the combined modality to the needle projection filter - mitk::AffineTransform3D::Pointer calibration = combinedModality->GetCalibration(); - if ( calibration.IsNotNull() ) + mitk::AffineTransform3D::Pointer usPlaneTransform = combinedModality->GetUSPlaneTransform(); + if (usPlaneTransform.IsNotNull()) { - m_NeedleProjectionFilter->SetTargetPlane(calibration); + m_NeedleProjectionFilter->SetTargetPlane(usPlaneTransform); } } else { MITK_WARN << "CombinedModality is null!"; } } void QmitkUSNavigationStepPunctuationIntervention::ClearZones() { m_Ui->riskStructuresRangeWidget->ClearZones(); } void QmitkUSNavigationStepPunctuationIntervention::UpdateBodyMarkerStatus(mitk::NavigationData::Pointer bodyMarker) { if ( bodyMarker.IsNull() ) { MITK_ERROR("QmitkUSAbstractNavigationStep")("QmitkUSNavigationStepPunctuationIntervention") << "Current Navigation Data for body marker of Combined Modality must not be null."; mitkThrow() << "Current Navigation Data for body marker of Combined Modality must not be null."; } bool valid = bodyMarker->IsDataValid(); // update body marker status label if (valid) { m_Ui->bodyMarkerTrackingStatusLabel->setStyleSheet( "background-color: #8bff8b; margin-right: 1em; margin-left: 1em; border: 1px solid grey"); m_Ui->bodyMarkerTrackingStatusLabel->setText("Body marker is inside the tracking volume."); } else { m_Ui->bodyMarkerTrackingStatusLabel->setStyleSheet( "background-color: #ff7878; margin-right: 1em; margin-left: 1em; border: 1px solid grey"); m_Ui->bodyMarkerTrackingStatusLabel->setText("Body marker is not inside the tracking volume."); } m_Ui->riskStructuresRangeGroupBox->setEnabled(valid); } void QmitkUSNavigationStepPunctuationIntervention::UpdateCriticalStructures(mitk::NavigationData::Pointer needle, mitk::PointSet::Pointer path) { // update the distances for the risk structures widget m_Ui->riskStructuresRangeWidget->UpdateDistancesToNeedlePosition(needle); //iterate through all zones for (mitk::DataStorage::SetOfObjects::ConstIterator it = m_ZoneNodes->Begin(); it != m_ZoneNodes->End(); ++it) { mitk::DataNode::Pointer currentNode = it->Value(); //get center point and radius float radius = -1; mitk::Point3D center; currentNode->GetFloatProperty("zone.size", radius); center = currentNode->GetData()->GetGeometry()->GetIndexToWorldTransform()->GetTranslation(); mitk::Point3D point0 = path->GetPoint(0); mitk::Point3D point1 = path->GetPoint(1); if (CheckSphereLineIntersection(center,radius,point0,point1)) {currentNode->SetColor(mitk::IGTColor_WARNING);} else {currentNode->SetColor(m_OldColors[currentNode]);} } } bool QmitkUSNavigationStepPunctuationIntervention::CheckSphereLineIntersection(mitk::Point3D& sphereOrigin, float& sphereRadius, mitk::Point3D& lineStart, mitk::Point3D& lineEnd) { double center[3] = {sphereOrigin[0],sphereOrigin[1],sphereOrigin[2]}; m_SphereSource->SetCenter(center); m_SphereSource->SetRadius(sphereRadius); m_SphereSource->Update(); m_OBBTree->SetDataSet(m_SphereSource->GetOutput()); m_OBBTree->BuildLocator(); double lineP0[3] = {lineStart[0], lineStart[1], lineStart[2]}; double lineP1[3] = {lineEnd[0], lineEnd[1], lineEnd[2]}; m_OBBTree->IntersectWithLine(lineP0, lineP1, m_IntersectPoints, nullptr); if (m_IntersectPoints->GetNumberOfPoints() > 0) {return true;} else {return false;} }