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/*=========================================================================
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Program: Image Guided Surgery Software Toolkit
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Module: $RCSfile: NeedleBiopsy.cxx,v $
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Date: $Date: 2009-06-12 15:23:31 $
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Version: $Revision: 1.3 $
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Copyright (c) ISC Insight Software Consortium. All rights reserved.
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See IGSTKCopyright.txt or http://www.igstk.org/copyright.htm for details.
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This software is distributed WITHOUT ANY WARRANTY; without even
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the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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PURPOSE. See the above copyright notices for more information.
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=========================================================================*/
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#include "NeedleBiopsy.h"
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#include "FL/Fl_File_Chooser.H"
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#include "FL/Fl_Input.H"
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#include "igstkEvents.h"
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#include "itksys/SystemTools.hxx"
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#include "itksys/Directory.hxx"
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#include "igstkTransformObserver.h"
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#include "PolarisTrackerConfigurationGUI.h"
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#include "AuroraTrackerConfigurationGUI.h"
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#include "MicronTrackerConfigurationGUI.h"
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/** -----------------------------------------------------------------
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* -----------------------------------------------------------------
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NeedleBiopsy::NeedleBiopsy() : m_LogFile()
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/** Setup logger, for all igstk components. */
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m_Logger = LoggerType::New();
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this->GetLogger()->SetTimeStampFormat( itk::LoggerBase::HUMANREADABLE );
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this->GetLogger()->SetHumanReadableFormat("%Y %b %d, %H:%M:%S");
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this->GetLogger()->SetPriorityLevel( LoggerType::INFO );
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/** Direct the application log message to the std::cout */
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itk::StdStreamLogOutput::Pointer m_LogCoutOutput
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= itk::StdStreamLogOutput::New();
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m_LogCoutOutput->SetStream( std::cout );
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this->GetLogger()->AddLogOutput( m_LogCoutOutput );
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/** Direct the igstk components log message to the file. */
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itk::StdStreamLogOutput::Pointer m_LogFileOutput
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= itk::StdStreamLogOutput::New();
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std::string logFileName;
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logFileName = "logNeedleBiopsy"
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+ itksys::SystemTools::GetCurrentDateTime( "_%Y_%m_%d_%H_%M_%S" ) + ".txt";
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m_LogFile.open( logFileName.c_str() );
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if( !m_LogFile.fail() )
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m_LogFileOutput->SetStream( m_LogFile );
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this->GetLogger()->AddLogOutput( m_LogFileOutput );
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//Return if fail to open the log file
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igstkLogMacro( DEBUG, "Problem opening Log file:"
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<< logFileName << "\n" );
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/** Initialize all member variables */
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m_ImageReader = ImageReaderType::New();
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m_LandmarkRegistration = RegistrationType::New();
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m_Annotation = igstk::Annotation2D::New();
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m_WorldReference = igstk::AxesObject::New();
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m_TrackerInitializerList.clear();
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m_Plan = new igstk::TreatmentPlan;
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/** Setting up spatial objects and their representations */
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m_NeedleTip = EllipsoidType::New();
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m_NeedleTipRepresentation = EllipsoidRepresentationType::New();
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m_NeedleTip->SetRadius( 5, 5, 5 );
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m_NeedleTipRepresentation->RequestSetEllipsoidObject( m_NeedleTip );
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m_NeedleTipRepresentation->SetColor(1.0,0.0,0.0);
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m_NeedleTipRepresentation->SetOpacity(1.0);
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m_Needle = CylinderType::New();
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m_NeedleRepresentation = CylinderRepresentationType::New();
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m_Needle->SetRadius( 1.5 );
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m_Needle->SetHeight( 100 );
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m_NeedleRepresentation->RequestSetCylinderObject( m_Needle );
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m_NeedleRepresentation->SetColor(0.0,1.0,0.0);
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m_NeedleRepresentation->SetOpacity(1.0);
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m_TargetPoint = EllipsoidType::New();
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m_TargetRepresentation = EllipsoidRepresentationType::New();
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m_TargetPoint->SetRadius( 6, 6, 6 );
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m_TargetRepresentation->RequestSetEllipsoidObject( m_TargetPoint );
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m_TargetRepresentation->SetColor( 1.0, 0.0, 0.0);
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m_TargetRepresentation->SetOpacity( 0.6 );
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m_EntryPoint = EllipsoidType::New();
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m_EntryRepresentation = EllipsoidRepresentationType::New();
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m_EntryPoint->SetRadius( 6, 6, 6 );
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m_EntryRepresentation->RequestSetEllipsoidObject( m_EntryPoint );
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m_EntryRepresentation->SetColor( 0.0, 0.0, 1.0);
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m_EntryRepresentation->SetOpacity( 0.6 );
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m_FiducialPoint = EllipsoidType::New();
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m_FiducialRepresentation = EllipsoidRepresentationType::New();
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m_FiducialPoint->SetRadius( 6, 6, 6 );
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m_FiducialRepresentation->RequestSetEllipsoidObject( m_FiducialPoint );
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m_FiducialRepresentation->SetColor( 0.0, 1.0, 0.0);
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m_FiducialRepresentation->SetOpacity( 0.6 );
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m_Path = PathType::New();
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point.SetPosition( 0, 0, 0);
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point.SetRadius( 2 );
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m_Path->AddPoint( point );
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m_Path->AddPoint( point );
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m_PathRepresentation.clear();
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for( int i=0; i<4; i++ )
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PathRepresentationType::Pointer rep = PathRepresentationType::New();
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rep->RequestSetTubeObject( m_Path );
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rep->SetColor( 0.0, 1.0, 0.0);
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rep->SetOpacity( 0.4 );
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m_PathRepresentation.push_back( rep );
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/** Creating observers and their call back functions */
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/** This observes picking event from view */
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m_ViewPickerObserver = LoadedObserverType::New();
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m_ViewPickerObserver->SetCallbackFunction( this, &NeedleBiopsy::Picking );
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/** This observes reslicing events from FourQuadrantView class */
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m_ViewResliceObserver = LoadedObserverType::New();
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m_ViewResliceObserver->SetCallbackFunction( this,
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&NeedleBiopsy::ResliceImage);
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* This observer catches the tracker configuration sent out by
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* TrackerConfiguration GUI
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m_TrackerConfigurationObserver = LoadedObserverType::New();
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m_TrackerConfigurationObserver->SetCallbackFunction( this,
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&NeedleBiopsy::RequestInitializeTracker);
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* This observer listens to the TrackerToolTransformUpdateEvent from
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* TrackerTool class, notice this event doesn't carry any payload, it
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* only functions as a ticker here to trigger image representation class
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* to do image reslicing according to the current tooltip location.
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* NeedleBiopsy::Tracking()
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m_TrackerToolUpdateObserver = LoadedObserverType::New();
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m_TrackerToolUpdateObserver->SetCallbackFunction( this,
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&NeedleBiopsy::Tracking);
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/** Create image slice representations */
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m_ImageRepresentation.clear();
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for (int i=0; i<6; i++)
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ImageRepresentationType::Pointer rep = ImageRepresentationType::New();
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m_ImageRepresentation.push_back( rep );
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/** -----------------------------------------------------------------
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* -----------------------------------------------------------------
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NeedleBiopsy::~NeedleBiopsy()
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m_TrackerInitializerList.clear();
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m_TrackerToolList.clear();
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/** -----------------------------------------------------------------
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* This methods asks for folder directory contains a single dicom
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* series. If it loads the image successfully, it will try loading
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* the previously saved treatment plan, in the same parent directory
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* which should be named "folderName_TreatmentPlan.igstk".
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* ReadTreatmentPlan()
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* WriteTreatmentPlan()
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* igstkTreatmentPlanIO
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* -----------------------------------------------------------------
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int NeedleBiopsy::RequestLoadImage()
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const char * directoryname = fl_dir_chooser("DICOM Volume directory","");
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if ( directoryname != NULL )
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igstkLogMacro( DEBUG,
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"Set ImageReader directory: " << directoryname << "\n" )
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m_ImageDir = directoryname;
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m_ImageReader->RequestSetDirectory( directoryname );
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igstkLogMacro( DEBUG, "ImageReader loading images... \n" )
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m_ImageReader->RequestReadImage();
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* IGSTK uses event for inter-components communication.
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* Event/observer model is used to replace the normal Get() method.
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* CTImageObserver here is defined by Macro in header file:
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* igstkObserverObjectMacro( CTImage,
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* igstk::CTImageReader::ImageModifiedEvent,
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* igstk::CTImageSpatialObject);
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* Refer to igstkMacros.h for more detail about this macro.
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CTImageObserver::Pointer m_CTImageObserver = CTImageObserver::New();
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m_ImageReader->AddObserver(igstk::CTImageReader::ImageModifiedEvent(),
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m_ImageReader->RequestGetImage(); // This will invoke the event
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if(m_CTImageObserver->GotCTImage())
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igstkLogMacro( DEBUG, "Image loaded...\n" )
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m_ImageSpatialObject = m_CTImageObserver->GetCTImage();
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this->ConnectImageRepresentation();
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this->ReadTreatmentPlan();
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igstkLogMacro( DEBUG, "Reading image failure...\n" )
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igstkLogMacro( DEBUG, "No directory is selected\n" )
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/** -----------------------------------------------------------------
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* This method should be invoked only when the Image has been loaded
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* -----------------------------------------------------------------
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void NeedleBiopsy::ConnectImageRepresentation()
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/** Setting up annotation and added to four views */
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m_Annotation->RequestSetAnnotationText( 2, "Georgetown ISIS Center" );
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for( int i=0; i<4; i++)
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ViewerGroup->m_Views[i]->RequestAddAnnotation2D( m_Annotation );
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* Pass image spatial object to image slice representation and set
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* the desired slice orientation for each representations, and then
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* add them to the views
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for( int i=0; i<6; i++)
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m_ImageRepresentation[i]->RequestSetImageSpatialObject(
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m_ImageSpatialObject );
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m_ImageRepresentation[0]->RequestSetOrientation(
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ImageRepresentationType::Axial );
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m_ImageRepresentation[1]->RequestSetOrientation(
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ImageRepresentationType::Sagittal );
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m_ImageRepresentation[2]->RequestSetOrientation(
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ImageRepresentationType::Coronal );
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m_ImageRepresentation[3]->RequestSetOrientation(
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ImageRepresentationType::Axial );
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m_ImageRepresentation[4]->RequestSetOrientation(
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ImageRepresentationType::Sagittal );
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m_ImageRepresentation[5]->RequestSetOrientation(
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ImageRepresentationType::Coronal );
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for ( int i=0; i<3; i++)
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ViewerGroup->m_Views[i]->RequestRemoveObject( m_ImageRepresentation[i] );
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ViewerGroup->m_Views[3]->RequestRemoveObject( m_ImageRepresentation[i+3] );
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ViewerGroup->m_Views[i]->RequestAddObject( m_ImageRepresentation[i] );
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ViewerGroup->m_Views[3]->RequestAddObject( m_ImageRepresentation[i+3] );
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* Add all the spatial object to the views
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* Notice the Copy() method is used for most of the representation
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* classes but not the path. This is because the underlying geometry
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* is fixed for those spatial object once it's created.But the path
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* will change it's shape, so we need to keep seperate pointer for
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* path representation in each view
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for ( int i=0; i<4; i++)
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igstk::View::Pointer view = ViewerGroup->m_Views[i];
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view->RequestAddObject( m_NeedleTipRepresentation->Copy() );
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view->RequestAddObject( m_NeedleRepresentation->Copy() );
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view->RequestAddObject( m_TargetRepresentation->Copy() );
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view->RequestAddObject( m_EntryRepresentation->Copy() );
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view->RequestAddObject( m_FiducialRepresentation->Copy() );
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view->RequestAddObject( m_PathRepresentation[i] );
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* Here we connect the scene graph
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* Here we created a virtual world reference system(as the root) and
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* attached all the objects as its children.
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* This is for the convenience in the following implementation. You
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* use any spatial object, view, tracker, or tracker tool as a
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* reference system in IGSTK. And you can create your own class to
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* use the coordinate system API by using this macro:
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* igstkCoordinateSystemClassInterfaceMacro()
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* igstkCoordinateSystemInterfaceMacros.h
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* igstkCoordinateSystem
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* igstkCoordinateSystemDelegator
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igstk::Transform transform;
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transform.SetToIdentity( igstk::TimeStamp::GetLongestPossibleTime() );
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for( int i=0; i<4; i++)
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ViewerGroup->m_Views[i]->RequestSetTransformAndParent(
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transform, m_WorldReference );
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m_ImageSpatialObject->RequestSetTransformAndParent(
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transform, m_WorldReference );
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m_EntryPoint->RequestSetTransformAndParent( transform, m_WorldReference );
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m_TargetPoint->RequestSetTransformAndParent( transform, m_WorldReference );
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m_FiducialPoint->RequestSetTransformAndParent( transform, m_WorldReference );
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m_Path->RequestSetTransformAndParent( transform, m_WorldReference );
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m_Needle->RequestSetTransformAndParent( transform, m_WorldReference );
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m_NeedleTip->RequestSetTransformAndParent( transform, m_WorldReference );
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/** Reset and enable the view */
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for( int i=0; i<4; i++)
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ViewerGroup->m_Views[i]->RequestResetCamera();
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ViewerGroup->m_Views[i]->SetRefreshRate( 30 );
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ViewerGroup->m_Views[i]->RequestStart();
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ViewerGroup->m_Displays[i]->RequestEnableInteractions();
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* Request information about the slice bounds. The answers will be
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* received in the form of events. This will be used to initialize
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* the reslicing sliders and initial slice position
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SliceBoundsObserver::Pointer boundsObs = SliceBoundsObserver::New();
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for ( int i=0; i<3; i++)
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m_ImageRepresentation[i]->AddObserver(
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igstk::IntegerBoundsEvent(), boundsObs);
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m_ImageRepresentation[i]->RequestGetSliceNumberBounds();
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if( boundsObs->GotSliceBounds() )
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const unsigned int min = boundsObs->GetSliceBounds().minimum;
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const unsigned int max = boundsObs->GetSliceBounds().maximum;
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const unsigned int slice =
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static_cast< unsigned int > ( (min + max) / 2.0 );
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m_ImageRepresentation[i]->RequestSetSliceNumber( slice );
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m_ImageRepresentation[i+3]->RequestSetSliceNumber( slice );
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ViewerGroup->m_Sliders[i]->minimum( min );
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ViewerGroup->m_Sliders[i]->maximum( max );
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ViewerGroup->m_Sliders[i]->value( slice );
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ViewerGroup->m_Sliders[i]->activate();
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/** Adding observer for picking event */
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for ( int i=0; i<3; i++)
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ViewerGroup->m_Views[i]->AddObserver(
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igstk::CoordinateSystemTransformToEvent(),
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m_ViewPickerObserver );
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/** Adding observer for slider bar reslicing event*/
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ViewerGroup->AddObserver( igstk::QuadrantViews::ReslicingEvent(),
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m_ViewResliceObserver );
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/** -----------------------------------------------------------------
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* Here we read the treatment plan. In this simple example
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* we assume there is one entry point, one target point, and at least
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* 3 fiducial points. Here is a sample format
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---------------------------------------------------------------------
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0.820425 -143.635 -186
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98.4887 -152.976 -181
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-1.89214 -148.996 -191
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-59.2006 -190.563 -191
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--------------------------------------------------------------------
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* igstkTreatmentPlanIO
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* -----------------------------------------------------------------
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void NeedleBiopsy::ReadTreatmentPlan()
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igstk::TreatmentPlanIO * reader = new igstk::TreatmentPlanIO;
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m_PlanFilename = m_ImageDir + "_TreatmentPlan.igstk";
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m_Plan = new igstk::TreatmentPlan;
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if (itksys::SystemTools::FileExists( m_PlanFilename.c_str()))
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reader->SetFileName( m_PlanFilename );
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if ( reader->RequestRead( ) )
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m_Plan = reader->GetTreatmentPlan();
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/** Populate the choice box */
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TPlanPointList->clear();
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TPlanPointList->add( "Entry" );
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TPlanPointList->add( "Target" );
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m_TrackerLandmarksContainer.clear();
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for( unsigned int i = 0; i < m_Plan->m_FiducialPoints.size(); i++ )
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sprintf( buf, "Fiducial%i", i+1 );
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TPlanPointList->add( buf );
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RegistrationType::LandmarkTrackerPointType p;
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m_TrackerLandmarksContainer.push_back(p);
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// Setting object position according to treatment plan
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m_EntryPoint->RequestSetTransformAndParent(
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PointToTransform( m_Plan->m_EntryPoint ), m_WorldReference);
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m_TargetPoint->RequestSetTransformAndParent(
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PointToTransform( m_Plan->m_TargetPoint ), m_WorldReference);
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TPlanPointList->value(0);
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ChangeSelectedTPlanPoint();
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/** -----------------------------------------------------------------
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* Overwrite the current treatment plan to the file
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* igstkTreatmentPlanIO
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*---------------------------------------------------------------------
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void NeedleBiopsy::WriteTreatmentPlan()
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igstk::TreatmentPlanIO * writer = new igstk::TreatmentPlanIO;
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writer->SetFileName( m_PlanFilename );
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writer->SetTreatmentPlan( m_Plan );
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writer->RequestWrite();
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/** -----------------------------------------------------------------
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* When changing the selection in the choice box, this function
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* reslices images to the current point location, and also show the
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* position in the annotation in blue. Whenever a point is selected
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* in the choice box, the picking event will update this point's location
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* NeedleBiopsy::Picking
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*---------------------------------------------------------------------
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void NeedleBiopsy::ChangeSelectedTPlanPoint()
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if ( TPlanPointList->size() == 0)
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* Check which point is selected, the first two are entry and target
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ImageSpatialObjectType::PointType point;
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int choice = TPlanPointList->value();
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point = m_Plan->m_EntryPoint;
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else if ( choice == 1 )
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point = m_Plan->m_TargetPoint;
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point = m_Plan->m_FiducialPoints[ choice-2];
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m_FiducialPoint->RequestSetTransformAndParent(
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PointToTransform(point), m_WorldReference );
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/** Display point position as annotation */
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sprintf( buf, "[%.2f, %.2f, %.2f]", point[0], point[1], point[2]);
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m_Annotation->RequestSetAnnotationText(0, buf);
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m_Annotation->RequestSetFontColor(0, 0, 0, 1.0);
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m_Annotation->RequestSetFontSize(0, 12);
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/** Reslice image to the selected point position */
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if( m_ImageSpatialObject->IsInside( point ) )
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ImageSpatialObjectType::IndexType index;
530
m_ImageSpatialObject->TransformPhysicalPointToIndex( point, index);
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igstkLogMacro( DEBUG, index <<"\n");
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ResliceImage( index );
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igstkLogMacro( DEBUG, "This point is not defined in the image...\n" )
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/** -----------------------------------------------------------------
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* Choose to connect to a tracker
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* A tracker specific GUI is initialized, and the observer is hooked
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* to it to catch the configuration. When the "confirm" button is
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* pressed, an event loaded with tracker configuration will be sent out.
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* And it will trigger the RequestInitializeTracker(), which does the
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* actual tracker initialization
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*---------------------------------------------------------------------
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void NeedleBiopsy::RequestConnectToTracker()
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RequestStopTracking();
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switch( ConnectToTrackerBtn->value() )
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igstk::TrackerConfiguration config = igstk::TrackerConfiguration();
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config.SetTrackerType( igstk::TrackerConfiguration::Polaris );
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PolarisTrackerConfigurationGUI * gui;
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m_TrackerConfigurationGUI = gui = new PolarisTrackerConfigurationGUI();
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m_TrackerConfigurationGUI->SetConfiguration( config );
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m_TrackerConfigurationGUI->RemoveAllObservers();
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m_TrackerConfigurationGUI->AddObserver(
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igstk::TrackerConfigurationGUIBase::ConfigurationEvent(),
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m_TrackerConfigurationObserver);
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igstk::TrackerConfiguration config = igstk::TrackerConfiguration();
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config.SetTrackerType( igstk::TrackerConfiguration::Aurora );
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AuroraTrackerConfigurationGUI * gui;
574
m_TrackerConfigurationGUI = gui = new AuroraTrackerConfigurationGUI();
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m_TrackerConfigurationGUI->SetConfiguration( config );
576
m_TrackerConfigurationGUI->RemoveAllObservers();
577
m_TrackerConfigurationGUI->AddObserver(
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igstk::TrackerConfigurationGUIBase::ConfigurationEvent(),
579
m_TrackerConfigurationObserver);
584
igstk::TrackerConfiguration config = igstk::TrackerConfiguration();
585
config.SetTrackerType( igstk::TrackerConfiguration::Micron );
586
MicronTrackerConfigurationGUI * gui;
587
m_TrackerConfigurationGUI = gui = new MicronTrackerConfigurationGUI();
588
m_TrackerConfigurationGUI->SetConfiguration( config );
589
m_TrackerConfigurationGUI->RemoveAllObservers();
590
m_TrackerConfigurationGUI->AddObserver(
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igstk::TrackerConfigurationGUIBase::ConfigurationEvent(),
592
m_TrackerConfigurationObserver);
598
/** -----------------------------------------------------------------
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* Call back function for ConfigurationEvent observer
600
*---------------------------------------------------------------------
602
void NeedleBiopsy::RequestInitializeTracker(const itk::EventObject & event)
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typedef igstk::TrackerConfigurationGUIBase GUIType;
605
if ( GUIType::ConfigurationEvent().CheckEvent( &event ) )
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GUIType::ConfigurationEvent *confEvent =
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( GUIType::ConfigurationEvent *) & event;
610
igstk::TrackerConfiguration tc = confEvent->Get();
612
m_TrackerInitializer = new igstk::TrackerInitializer;
613
m_TrackerInitializer->SetTrackerConfiguration( & tc );
615
if ( m_TrackerInitializer->RequestInitializeTracker() )
617
igstk::Tracker::Pointer tracker = m_TrackerInitializer->GetTracker();
618
igstk::TrackerTool::Pointer tool =
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m_TrackerInitializer->GetNonReferenceToolList()[0];
620
igstk::TrackerTool::Pointer refTool =
621
m_TrackerInitializer->GetReferenceTool();
623
/** Connect the scene graph with an identity transform first */
624
igstk::Transform transform;
625
transform.SetToIdentity( igstk::TimeStamp::GetLongestPossibleTime() );
626
if ( m_TrackerInitializer->HasReferenceTool() )
628
refTool->RequestSetTransformAndParent(transform, m_WorldReference);
632
tracker->RequestSetTransformAndParent(transform, m_WorldReference);
635
/** Now who the registration window and initialize it */
636
RegistrationWindow->show();
637
FiducialNumber->clear();
638
m_TrackerLandmarksContainer.clear();
640
for ( unsigned int i=0; i<m_Plan->m_FiducialPoints.size(); i++)
642
sprintf( buf, "%d", i+1 );
643
FiducialNumber->add(buf);
644
RegistrationType::LandmarkTrackerPointType p;
645
m_TrackerLandmarksContainer.push_back(p);
649
* Set the tracker and image fiducial landmark to the first point
650
* and reslice the image to show this fiducial point
652
FiducialNumber->value(0);
653
TPlanPointList->value(2);
654
ChangeSelectedTPlanPoint();
659
/** -----------------------------------------------------------------
660
* Call this method every time we successfully connect or disconnect to
661
* a tracker. This updates the available tracker and tracker tool
662
* in the GUI list as well as internal pointer list.
663
*---------------------------------------------------------------------
665
void NeedleBiopsy::UpdateTrackerAndTrackerToolList()
667
TrackerList->clear();
668
TrackerToolList->clear();
669
m_TrackerToolList.clear();
672
for ( unsigned int i=0; i<m_TrackerInitializerList.size(); i++)
675
sprintf(buf, "%d", i+1);
678
m_TrackerInitializerList[i]->GetTrackerTypeAsString() + "]";
679
TrackerList->add( s.c_str() );
680
std::vector< igstk::TrackerTool::Pointer > toolList =
681
m_TrackerInitializerList[i]->GetNonReferenceToolList();
682
for ( unsigned int j=0; j< toolList.size(); j++)
685
sprintf(buf,"%d", ++n);
688
m_TrackerInitializerList[i]->GetTrackerTypeAsString() + "]";
689
TrackerToolList->add( s.c_str() );
690
m_TrackerToolList.push_back( toolList[j] );
696
/** -----------------------------------------------------------------
697
* Disconnect a tracker. After disconnecting it, set the active tool
698
* to the first available tool
699
*---------------------------------------------------------------------
701
void NeedleBiopsy::RequestDisconnetTracker()
703
RequestStopTracking();
704
unsigned int n = TrackerList->value();
705
if ( n < m_TrackerInitializerList.size() )
707
m_TrackerInitializerList[n]->StopAndCloseTracker();
708
m_TrackerInitializerList.erase( m_TrackerInitializerList.begin() + n );
709
UpdateTrackerAndTrackerToolList();
710
if (m_TrackerInitializerList.size()>0)
712
TrackerList->value(0);
713
TrackerToolList->value(0);
715
ChangeActiveTrackerTool();
719
/** -----------------------------------------------------------------
720
* Hot switch the active tool, the one that drives the reslicing and
721
* needle display. The reslicing is done by using an observer listening
722
* to the TrackerToolTransformUpdateEvent, and the call back function
723
* will get the tool tip position in the image space and reslice image
724
* to that point. Refer to:
725
* NeedleBiopsy::Tracking
726
* First, we stop the tracking and disconnect the observer from other tools
727
* Second, we connect observer to the selected tool
728
* Finally, we attach spatial objects representing the needle to this tool
729
* and restart the tracking again
730
*---------------------------------------------------------------------
732
void NeedleBiopsy::ChangeActiveTrackerTool()
734
RequestStopTracking();
735
itksys::SystemTools::Delay( 500 );
737
if (m_TrackerToolList.size() != 0)
739
for (unsigned int i=0; i<m_TrackerToolList.size(); i++)
741
m_TrackerToolList[i]->RemoveAllObservers();
743
m_ActiveTool = m_TrackerToolList[ TrackerToolList->value()];
745
m_ActiveTool->AddObserver(
746
igstk::TrackerToolTransformUpdateEvent(), m_TrackerToolUpdateObserver);
748
igstk::Transform transform;
749
transform.SetToIdentity(igstk::TimeStamp::GetLongestPossibleTime());
750
m_Needle->RequestDetachFromParent();
751
m_NeedleTip->RequestDetachFromParent();
752
m_Needle->RequestSetTransformAndParent( transform, m_ActiveTool);
753
m_NeedleTip->RequestSetTransformAndParent( transform, m_ActiveTool);
755
RequestStartTracking();
758
/** -----------------------------------------------------------------
759
* Call back functions for registration window. Every time user clicks
760
* on the set fiducial point button, it will read from the recently
761
* initialized tracker's first non-reference tool. The reading will
762
* serve as a tracker landmark point for registration.
763
* This will automatic jump to the next fiducial point for user to set
764
*---------------------------------------------------------------------
766
void NeedleBiopsy::SetTrackerFiducialPoint()
768
igstk::TrackerTool::Pointer tool =
769
m_TrackerInitializer->GetNonReferenceToolList()[0];
771
typedef igstk::TransformObserver ObserverType;
772
ObserverType::Pointer transformObserver = ObserverType::New();
773
transformObserver->ObserveTransformEventsFrom( tool );
774
transformObserver->Clear();
775
tool->RequestComputeTransformTo( m_WorldReference );
776
if ( transformObserver->GotTransform() )
778
int n = FiducialNumber->value();
779
int m = FiducialNumber->size();
780
m_TrackerLandmarksContainer[n] =
781
TransformToPoint( transformObserver->GetTransform() );
782
std::cout << m_TrackerLandmarksContainer[n] <<"\n";
785
FiducialNumber->value(n+1);
786
TPlanPointList->value(n+3);
787
ChangeSelectedTPlanPoint();
792
/** -----------------------------------------------------------------
793
* Pair points 3D landmark registration
794
* Image landmarks are from treatment plan. Refer to:
797
* tracker landmarks are set in the registration window. Refer to:
798
* SetTrackerFiducialPoint
799
*---------------------------------------------------------------------
801
void NeedleBiopsy::RequestRegistration()
803
m_LandmarkRegistration->RequestResetRegistration();
804
for( unsigned int i=0; i< m_TrackerLandmarksContainer.size(); i++)
806
m_LandmarkRegistration->RequestAddImageLandmarkPoint(
807
m_Plan->m_FiducialPoints[i] );
808
m_LandmarkRegistration->RequestAddTrackerLandmarkPoint(
809
m_TrackerLandmarksContainer[i] );
812
m_LandmarkRegistration->RequestComputeTransform();
814
igstk::TransformObserver::Pointer lrtcb = igstk::TransformObserver::New();
815
lrtcb->ObserveTransformEventsFrom( m_LandmarkRegistration );
818
m_LandmarkRegistration->RequestGetTransformFromTrackerToImage();
820
if( lrtcb->GotTransform() )
822
RegistrationErrorObserver::Pointer lRmscb =
823
RegistrationErrorObserver::New();
824
m_LandmarkRegistration->AddObserver( igstk::DoubleTypeEvent(), lRmscb );
825
m_LandmarkRegistration->RequestGetRMSError();
826
if( lRmscb->GotRegistrationError() )
828
std::cout << "\nRegistration Error" <<
829
lRmscb->GetRegistrationError() << "\n";
832
igstk::Transform transform = lrtcb->GetTransform();
833
std::cout << transform << "\n";
834
if ( m_TrackerInitializer->HasReferenceTool() )
836
m_TrackerInitializer->GetReferenceTool()
837
->RequestSetTransformAndParent(transform, m_WorldReference);
841
m_TrackerInitializer->GetTracker()
842
->RequestSetTransformAndParent(transform, m_WorldReference);
846
* Only when a tracker is registered with the image, it will show up
847
* on the gui as available. Otherwise it will be disconnected
849
m_TrackerInitializerList.push_back( m_TrackerInitializer );
850
UpdateTrackerAndTrackerToolList();
851
TrackerList->value(m_TrackerInitializerList.size()-1);
852
TrackerToolList->value(m_TrackerInitializerList.size()-1);
853
ChangeActiveTrackerTool();
854
RequestStartTracking();
858
m_TrackerInitializer->StopAndCloseTracker();
863
/** -----------------------------------------------------------------
864
* Start tracking of all the connected trackers
865
*---------------------------------------------------------------------
867
void NeedleBiopsy::RequestStartTracking()
869
for (unsigned int i=0; i<m_TrackerInitializerList.size(); i++)
871
m_TrackerInitializerList[i]->GetTracker()->RequestStartTracking();
874
TrackingBtn->label("Stop");
875
TrackingBtn->value(1);
876
ControlGroup->redraw();
879
/** -----------------------------------------------------------------
880
* Stop tracking of all the connected trackers
881
*---------------------------------------------------------------------
883
void NeedleBiopsy::RequestStopTracking()
885
for (unsigned int i=0; i<m_TrackerInitializerList.size(); i++)
887
m_TrackerInitializerList[i]->GetTracker()->RequestStopTracking();
890
TrackingBtn->label("Tracking");
891
TrackingBtn->value(0);
892
ControlGroup->redraw();
895
/** -----------------------------------------------------------------
896
* Callback function for observer listening to the slider bar
898
*---------------------------------------------------------------------
900
void NeedleBiopsy::ResliceImage( const itk::EventObject & event )
903
if ( igstk::QuadrantViews::ReslicingEvent().CheckEvent( &event ) )
905
igstk::QuadrantViews::ReslicingEvent *resliceEvent =
906
( igstk::QuadrantViews::ReslicingEvent *) & event;
907
this->ResliceImage( resliceEvent->Get() );
912
/** -----------------------------------------------------------------
913
* Methods for reslicing images given an index number
914
*---------------------------------------------------------------------
916
void NeedleBiopsy::ResliceImage ( IndexType index )
918
m_ImageRepresentation[0]->RequestSetSliceNumber( index[2] );
919
m_ImageRepresentation[1]->RequestSetSliceNumber( index[0] );
920
m_ImageRepresentation[2]->RequestSetSliceNumber( index[1] );
922
m_ImageRepresentation[3]->RequestSetSliceNumber( index[2] );
923
m_ImageRepresentation[4]->RequestSetSliceNumber( index[0] );
924
m_ImageRepresentation[5]->RequestSetSliceNumber( index[1] );
926
ViewerGroup->m_AxialSlider->value( index[2] );
927
ViewerGroup->m_SagittalSlider->value( index[0] );
928
ViewerGroup->m_CoronalSlider->value( index[1] );
930
this->ViewerGroup->redraw();
935
/** -----------------------------------------------------------------
936
* Callback function for picking event.
937
* Upon receiving a valid picking event, this method will change the
938
* value of currently selected treatment plan point, reslice the image
939
* to that location, update the annotation with the new point position,
940
* and write the modified treatment plan to the file.
941
*---------------------------------------------------------------------
943
void NeedleBiopsy::Picking( const itk::EventObject & event)
945
if ( igstk::CoordinateSystemTransformToEvent().CheckEvent( &event ) )
947
typedef igstk::CoordinateSystemTransformToEvent TransformEventType;
948
const TransformEventType * tmevent =
949
dynamic_cast< const TransformEventType *>( & event );
951
igstk::CoordinateSystemTransformToResult transformCarrier = tmevent->Get();
952
igstk::Transform transform = transformCarrier.GetTransform();
953
ImageSpatialObjectType::PointType point = TransformToPoint( transform );
955
if( m_ImageSpatialObject->IsInside( point ) )
957
int choice = TPlanPointList->value();
961
m_EntryPoint->RequestSetTransformAndParent(
962
transform , m_WorldReference );
963
m_Plan->m_EntryPoint = point;
966
else if ( choice == 1 )
968
m_TargetPoint->RequestSetTransformAndParent(
969
transform, m_WorldReference );
970
m_Plan->m_TargetPoint = point;
975
m_FiducialPoint->RequestSetTransformAndParent(
976
transform, m_WorldReference );
977
m_Plan->m_FiducialPoints[ choice-2] = point;
980
/** Update annotation */
982
sprintf( buf, "[%.2f, %.2f, %.2f]", point[0], point[1], point[2]);
983
m_Annotation->RequestSetAnnotationText(0, buf);
984
m_Annotation->RequestSetFontColor(0, 1.0, 0, 0);
985
m_Annotation->RequestSetFontSize(0, 12);
987
/** Wirte the updated plan to file */
988
this->WriteTreatmentPlan();
991
ImageSpatialObjectType::IndexType index;
992
m_ImageSpatialObject->TransformPhysicalPointToIndex( point, index);
993
igstkLogMacro( DEBUG, index <<"\n")
994
ResliceImage( index );
998
igstkLogMacro( DEBUG, "Picked point outside image...\n" )
1003
/** -----------------------------------------------------------------
1004
* Every time we modify the entry point or target point, we need to
1005
* rebuild the geometry of the path, and add them to the View again
1006
*---------------------------------------------------------------------
1008
void NeedleBiopsy::UpdatePath()
1012
TubePointType point;
1013
igstk::Transform::VectorType v;
1015
v = ( PointToTransform( m_Plan->m_EntryPoint) ).GetTranslation();
1016
point.SetPosition( v[0], v[1], v[2]);
1017
point.SetRadius( 2 );
1018
m_Path->AddPoint( point );
1020
v = ( PointToTransform( m_Plan->m_TargetPoint) ).GetTranslation();
1021
point.SetPosition( v[0], v[1], v[2]);
1022
point.SetRadius( 2.1 );
1023
m_Path->AddPoint( point );
1026
for (int i=0; i<4; i++)
1028
ViewerGroup->m_Views[i]->RequestRemoveObject( m_PathRepresentation[i] );
1029
m_PathRepresentation[i]->RequestSetTubeObject( NULL );
1030
m_PathRepresentation[i]->RequestSetTubeObject( m_Path );
1031
m_PathRepresentation[i]->SetColor( 0.0, 1.0, 0.0 );
1032
m_PathRepresentation[i]->SetOpacity( 0.5 );
1033
ViewerGroup->m_Views[i]->RequestAddObject( m_PathRepresentation[i] );
1038
/** -----------------------------------------------------------------
1039
* Callback function for TrackerToolTransformUpdateEvent
1040
* This function computes the transform of the tooltip location in
1041
* the image space (WorldReference is essential image coordinate system
1042
* since image is attached to WorldReference using an identity transform),
1043
* and reslice image to that tip location
1044
*---------------------------------------------------------------------
1047
void NeedleBiopsy::Tracking(const itk::EventObject & event )
1049
if ( igstk::TrackerToolTransformUpdateEvent().CheckEvent( &event ) )
1051
typedef igstk::TransformObserver ObserverType;
1052
ObserverType::Pointer transformObserver = ObserverType::New();
1053
transformObserver->ObserveTransformEventsFrom( m_ActiveTool );
1054
transformObserver->Clear();
1055
m_ActiveTool->RequestComputeTransformTo( m_WorldReference );
1056
if ( transformObserver->GotTransform() )
1058
ImageSpatialObjectType::PointType point =
1059
TransformToPoint( transformObserver->GetTransform() );
1061
if( m_ImageSpatialObject->IsInside( point ) )
1063
ImageSpatialObjectType::IndexType index;
1064
m_ImageSpatialObject->TransformPhysicalPointToIndex( point, index);
1065
ResliceImage( index );
added
removed
Examples/NeedleBiopsy/NeedleBiopsy.cxx
