Merge branch 'ScoutRTUIDevelOptim' into 'ScoutRTUIDevel'
First integration of Automatic Registration is running (on Approve button).... See merge request cpt_bioeng/drt!20
This commit is contained in:
@ -2,6 +2,8 @@ cmake_minimum_required(VERSION 2.8.12)
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SET(LIB_NAME itkDTRrecon)
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add_subdirectory(autoreg)
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find_package(ITK REQUIRED)
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include(${ITK_USE_FILE})
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INCLUDE_DIRECTORIES(${ITK_INCLUDE_DIRS})
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@ -34,6 +36,7 @@ SET(LINK_LIBS
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${VTK_LIBRARIES}
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${ITK_LIBRARIES}
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gdcmMSFF
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autoreg
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)
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TARGET_LINK_LIBRARIES(
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@ -531,6 +531,8 @@ TransformMetaInformation (){
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m_CurrentTransform.Fill(0.);
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m_DegreeOfFreedom = tDegreeOfFreedomEnum::UNKNOWN;
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}
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void
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@ -11,15 +11,70 @@
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namespace itk
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{
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typedef enum eProjectionOrientationType
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{NA = 0, LAT=2, PA=1}
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tProjOrientationType;
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typedef enum eProjectionOrientationType{
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NA = 0,
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LAT=2,
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PA=1
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} tProjOrientationType;
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/** Enum type for Orientation */
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typedef enum eImageOrientationType
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{NotDefined = 0, HFS = 1, FFS = 2}
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tPatOrientation;
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typedef enum eImageOrientationType{
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NotDefined = 0,
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HFS = 1,
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FFS = 2
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} tPatOrientation;
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typedef enum eDegreeOfFreedomType {
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UNKNOWN = 0,
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THREE_DOF,
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SIX_DOF,
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X_ONLY,
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Y_ONLY,
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Z_ONLY,
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ROTATION_ONLY,
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OTHER
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} tDegreeOfFreedomEnum;
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inline int GetNumberOfDOF(eDegreeOfFreedomType dof)
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{
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switch (dof) {
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case SIX_DOF:
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return 6;
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break;
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case THREE_DOF:
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case ROTATION_ONLY:
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return 3;
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break;
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case X_ONLY:
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case Y_ONLY:
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case Z_ONLY:
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return 1;
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break;
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default:
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return 0;
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}
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}
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class DegreeOfFreedom : public itk::Object {
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public:
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typedef DegreeOfFreedom Self;
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typedef itk::Object Superclass;
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typedef itk::SmartPointer<Self> Pointer;
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itkNewMacro(Self);
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protected:
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bool
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m_TranslationX,
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m_TranslationY,
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m_TranslationZ,
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m_RotationX,
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m_RotationY,
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m_RotationZ;
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tDegreeOfFreedomEnum m_dof;
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};
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class TopogramImageMetaInformation :
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public itk::Object{
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@ -490,6 +545,8 @@ public:
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itkSetMacro(CurrentTransform,TransformMatrixType);
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itkGetMacro(CurrentTransform,TransformMatrixType);
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itkSetEnumMacro(DegreeOfFreedom, tDegreeOfFreedomEnum);
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itkGetEnumMacro(DegreeOfFreedom, tDegreeOfFreedomEnum);
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protected:
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@ -503,6 +560,8 @@ protected:
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m_ReferenceTransform,
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m_CurrentTransform;
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tDegreeOfFreedomEnum
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m_DegreeOfFreedom;
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/** Default Constructor **/
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TransformMetaInformation ();
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@ -14,6 +14,7 @@ gfattori 08.11.2021
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#include "itkImageProcessor.h"
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#include "itkCreateObjectFunction.h"
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#include "itkDRTHelpers.h"
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#include "itkVersion.h"
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#include <gdcmReader.h>
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#include <itkMatrix.h>
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@ -24,6 +25,8 @@ gfattori 08.11.2021
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#include "itkOrientImageFilter.h"
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#include <gdcmIPPSorter.h>
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#include "itkTimeProbesCollectorBase.h"
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#include <string>
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@ -31,34 +34,6 @@ gfattori 08.11.2021
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namespace itk
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{
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/* this is in the end a IEC to HFS...
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* but we keep this for ourselves...
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*/
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static double Standard_DRT2LPS [9] = {
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1,0,0,
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0,0,-1,
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0,1,0 };
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static double PAElementsIEC[9] = {
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1, 0, 0,
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0, -1, 0,
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0, 0, -1 };
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static double LATElementsIEC[9] = {
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0, 0, -1,
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0, -1, 0,
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-1, 0, 0};
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static double HFS2IEC[9] = {
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1, 0, 0,
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0, 0, 1,
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0, -1, 0};
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static double FFS2IEC[9] = {
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-1, 0, 0,
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0, 0, -1,
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0, -1, 0};
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//FUNCTION DECLARATION NECESSARY FOR COPY/PASTE FROM vtkGDCMImageReader
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// const char *gGetStringValueFromTag(const gdcm::Tag& t, const gdcm::DataSet& ds);
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@ -97,6 +72,8 @@ itkImageProcessor::itkImageProcessor()
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// TZero[0]=TZero[1]=TZero[2]=0.;
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// RZero[0]=RZero[1]=RZero[2]=0.;
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toVTK2D1 = ITKtoVTKFilterType::New();
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toVTK2D2 = ITKtoVTKFilterType::New();
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toVTKLocalizer1 = ITKtoVTKFilterType::New();
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@ -217,7 +194,37 @@ itkImageProcessor::itkImageProcessor()
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// };
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// setup the Automatic Registration
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metric = MetricType::New();
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mimetric = MIMetricType::New();
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optimizer = OptimizerType::New();
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amoebaoptimizer = AmoebaOptimizerType::New();
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optimizerObserver = CommandIterationUpdate::New();
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exhaustiveOptimizer = ExhaustiveOptimizerType::New();
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exhaustiveOptimizerObserver = ExhaustiveCommandIterationUpdate::New();
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registration = RegistrationType::New();
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if (m_UseMutualInformation) {
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registration->SetMetric(mimetric);
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} else {
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registration->SetMetric(metric);
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}
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registration->SetOptimizer(optimizer);
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registration->SetTransform1(transform1);
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registration->SetTransform2(transform2);
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registration->SetInterpolator1(interpolator1);
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registration->SetInterpolator2(interpolator2);
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m_UseExhaustiveOptmizer = false; //if the exhaustive optimizer shal be used, ovverrides ameoba
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m_UseAmeobaOptimizer = false; //if the ameoba optimzer shall be used, otherwise Powell. Overriden by Exhaustive option.
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m_UseFullROI = true; // if the full image ROI shall be used
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m_UseMutualInformation = false; //oterwise NCC is used
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m_UseDumptoFile = false; //If each (!) optimzer result shall be dumpped into a file.
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}
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itkImageProcessor::~itkImageProcessor()
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@ -257,6 +264,17 @@ double itkImageProcessor::GetSCD2(){
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m_DRTImage1MetaInfo ->GetSCD();
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}
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void itkImageProcessor::SetDegreeOfFreedom(tDegreeOfFreedomEnum dof)
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{
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m_TransformMetaInfo->SetDegreeOfFreedom(dof);
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}
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tDegreeOfFreedomEnum
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itkImageProcessor::GetDegreeOfFreedom()
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{
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return m_TransformMetaInfo->GetDegreeOfFreedom();
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}
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void itkImageProcessor::SetCustom_ImportTransform(double dTx,
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double dTy,
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double dTz,
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@ -384,8 +402,6 @@ void itkImageProcessor::SetCustom_2Dsize(int nX1, int nY1,int nX2,int nY2)
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void itkImageProcessor::SetCustom_UpdateMetaInfo(){
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this->UpdateProjectionGeometryMeta();
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}
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@ -1254,6 +1270,35 @@ itkImageProcessor::MapTransformToNewOrigin(
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return m_OutputTransform;
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}
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// This External User Transform thing need to be checked out
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void itkImageProcessor::CalculateExternalUserTransform(TransformType::Pointer transform, DRTImageMetaInformation::Pointer imageMetaInfo)
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{
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//crude hack to get from internal transform in LPS to external transform in IEC.
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//result is stored in m_TransformMetaInfo
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//TODO: support for projectionTransformCenter and userTransformCenter which are not the same
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//currentlz we support only pFakeIsoLPS situations.
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InternalImageType::DirectionType LPStoIEC_Directions;
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LPStoIEC_Directions = m_CTMetaInfo->GetLPS2IECDirections();
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auto parameters = transform->GetParameters();
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ImageType3D::PointType translationUser;
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translationUser[0] = parameters[3];
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translationUser[1] = parameters[4];
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translationUser[2] = parameters[5];
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ImageType3D::PointType rotationUser;
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rotationUser[0] = parameters[0];
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rotationUser[1] = parameters[1];
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rotationUser[2] = parameters[2];
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m_TransformMetaInfo->SetUserTranslations(LPStoIEC_Directions * translationUser);
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m_TransformMetaInfo->SetUserRotations(LPStoIEC_Directions * rotationUser);
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}
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itkImageProcessor::TransformType::Pointer
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itkImageProcessor::CalculateInternalTransform(
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ImageType3D::PointType m_TranslationOffset, //IEC
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@ -1323,6 +1368,362 @@ itkImageProcessor::CalculateInternalTransform(
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m_OutputTransform;
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}
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void itkImageProcessor::InitializeRegistration(int maximumIteration, double stepLength, double maxTranslation, eDegreeOfFreedomType dof)
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{
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std::cout << "*" << __COMPACT_PRETTY_FUNCTION__ << std::endl;
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if (!m_PASourceDupli) {
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itkExceptionMacro(<< "PA topogram not present");
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}
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if (!m_LATSourceDupli) {
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itkExceptionMacro(<< "LAT topogram not present");
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}
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if (!m_VolumeSourceDupli) {
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itkExceptionMacro(<< "CT data not present");
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}
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metric->ComputeGradientOff();
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metric->SetSubtractMean(true);
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metric->SetMaxTranslation(maxTranslation);
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m_TransformMetaInfo->SetDegreeOfFreedom(dof);
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mimetric->ComputeGradientOff();
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if (verbose) {
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metric->DebugOn();
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}
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registration->SetFixedImage1(m_PASourceDupli->GetOutput());
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registration->SetFixedImage2(m_LATSourceDupli->GetOutput());
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registration->SetMovingImage(m_VolumeSourceDupli->GetOutput());
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//TODO: Here we could set the ROI for image registartion
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auto region1 = m_PASourceDupli->GetOutput()->GetBufferedRegion();
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auto region2 = m_LATSourceDupli->GetOutput()->GetBufferedRegion();
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// bool setROI = false;
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// if (setROI) {
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// auto index1 = region1.GetIndex();
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// auto size1 = region1.GetSize();
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// auto point1 = m_PASourceDupli->GetOutput()->GetOrigin();
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// index1[0] = size1[0] / 2 - 50;
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// index1[1] = size1[1] / 2 - 50;
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||||
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// size1[0] = 100;
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// size1[1] = 100;
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// size1[2] = 1;
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// region1.SetIndex(index1);
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// region1.SetSize(size1);
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// }
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registration->SetFixedImageRegion1(region1);
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registration->SetFixedImageRegion2(region2);
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registration->SetTransformMetaInfo(m_TransformMetaInfo);
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||||
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registration->SetFilter1(filter1);
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registration->SetFilter2(filter2);
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//CalculateInternalTransform(transform1, m_DRTImage1MetaInfo);
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/********* BEGIN CALCULATION OF INTERNAL TRANSFORM FOR PROJ1 *********/
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||||
ImageType3D::PointType ZeroPoint;
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||||
ZeroPoint.Fill(0.);
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||||
InternalImageType::DirectionType IECtoLPS_Directions;
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||||
IECtoLPS_Directions =
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m_CTMetaInfo->GetLPS2IECDirections().GetTranspose();
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TransformType::Pointer CurrTransform;
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if(m_RTMetaInfo == NULL)
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||||
{
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||||
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||||
//AAAAAA TODOOOOO CERCA
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||||
ImageType3D::PointType pFakeIsoLPS =
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||||
m_DRTImage1MetaInfo->GetProjectionOriginLPS();
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||||
//ImageType3D::PointType pFakeIsoLPS =
|
||||
// m_CTMetaInfo->GetProjectionOriginLPS(
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||||
// m_DRTGeometryMetaInfo->GetProjectionCenter1());
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||||
CurrTransform =
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||||
CalculateInternalTransform(
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||||
ZeroPoint,
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ZeroPoint,
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m_TransformMetaInfo->GetTranslations(),
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||||
m_TransformMetaInfo->GetRotations(),
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m_DRTImage1MetaInfo->GetProjectionOriginLPS(),
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||||
pFakeIsoLPS,
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||||
ZeroPoint,
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IECtoLPS_Directions
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||||
);
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||||
} else {
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||||
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||||
CurrTransform =
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||||
CalculateInternalTransform(
|
||||
ZeroPoint ,
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||||
m_DRTGeometryMetaInfo->GetIECS2IECScannerR(),
|
||||
m_TransformMetaInfo->GetTranslations(),
|
||||
m_TransformMetaInfo->GetRotations(),
|
||||
m_DRTImage1MetaInfo->GetProjectionOriginLPS(),
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||||
m_RTMetaInfo->GetIsocenterLPS() - m_CTMetaInfo->GetImportOffset(),
|
||||
m_CTMetaInfo->GetImportOffset(),
|
||||
IECtoLPS_Directions
|
||||
);
|
||||
|
||||
}
|
||||
|
||||
|
||||
transform1->SetComputeZYX(true);
|
||||
transform1->SetIdentity();
|
||||
transform1->SetTranslation(
|
||||
CurrTransform->GetTranslation());
|
||||
transform1->SetRotation(
|
||||
CurrTransform->GetAngleX(),
|
||||
CurrTransform->GetAngleY(),
|
||||
CurrTransform->GetAngleZ()
|
||||
);
|
||||
transform1->SetCenter(
|
||||
m_DRTImage1MetaInfo->GetProjectionOriginLPSZero() );
|
||||
/********* END OF CALCULATE INTERNAL TRANSFORM FOR PROJ1 *********/
|
||||
|
||||
|
||||
//CalculateInternalTransform(transform2, m_DRTImage2MetaInfo);
|
||||
/********* BEGIN CALCULATION OF INTERNAL TRANSFORM FOR PROJ2 *********/
|
||||
if(m_RTMetaInfo == NULL)
|
||||
{
|
||||
ImageType3D::PointType pFakeIsoLPS =
|
||||
m_DRTImage2MetaInfo->GetProjectionOriginLPS();
|
||||
|
||||
//ImageType3D::PointType pFakeIsoLPS =
|
||||
// m_CTMetaInfo->GetProjectionOriginLPS(
|
||||
// m_DRTGeometryMetaInfo->GetProjectionCenter2());
|
||||
|
||||
|
||||
|
||||
CurrTransform =
|
||||
CalculateInternalTransform(
|
||||
ZeroPoint,
|
||||
ZeroPoint,
|
||||
m_TransformMetaInfo->GetTranslations(),
|
||||
m_TransformMetaInfo->GetRotations(),
|
||||
m_DRTImage2MetaInfo->GetProjectionOriginLPS(),
|
||||
pFakeIsoLPS,
|
||||
ZeroPoint,
|
||||
IECtoLPS_Directions
|
||||
);
|
||||
} else {
|
||||
|
||||
CurrTransform =
|
||||
CalculateInternalTransform(
|
||||
ZeroPoint ,
|
||||
m_DRTGeometryMetaInfo->GetIECS2IECScannerR(),
|
||||
m_TransformMetaInfo->GetTranslations(),
|
||||
m_TransformMetaInfo->GetRotations(),
|
||||
m_DRTImage2MetaInfo->GetProjectionOriginLPS(),
|
||||
m_RTMetaInfo->GetIsocenterLPS() - m_CTMetaInfo->GetImportOffset(),
|
||||
m_CTMetaInfo->GetImportOffset(),
|
||||
IECtoLPS_Directions
|
||||
);
|
||||
|
||||
}
|
||||
transform2->SetComputeZYX(true);
|
||||
transform2->SetIdentity();
|
||||
transform2->SetTranslation(
|
||||
CurrTransform->GetTranslation());
|
||||
transform2->SetRotation(
|
||||
CurrTransform->GetAngleX(),
|
||||
CurrTransform->GetAngleY(),
|
||||
CurrTransform->GetAngleZ()
|
||||
);
|
||||
transform2->SetCenter(
|
||||
m_DRTImage2MetaInfo->GetProjectionOriginLPSZero() );
|
||||
/********* END OF CALCULATE INTERNAL TRANSFORM FOR PROJ1 *********/
|
||||
|
||||
|
||||
if (verbose) {
|
||||
registration->DebugOn();
|
||||
registration->Print(std::cout);
|
||||
}
|
||||
|
||||
if (!m_UseExhaustiveOptmizer) {
|
||||
if (!m_UseAmeobaOptimizer) {
|
||||
|
||||
// The metric will return 0 or a "large" negative number in case of high correspondence of the images
|
||||
// Thus, we need to minimze
|
||||
optimizer->SetMaximize(false); // for NCC and MI
|
||||
optimizer->SetMaximumIteration(maximumIteration);
|
||||
optimizer->SetMaximumLineIteration(4); // for Powell's method
|
||||
optimizer->SetStepLength(stepLength);
|
||||
optimizer->SetStepTolerance(0.01);
|
||||
optimizer->SetValueTolerance(0.000002);
|
||||
if (verbose) {
|
||||
optimizer->DebugOn();
|
||||
optimizer->Print(std::cout);
|
||||
}
|
||||
|
||||
optimizer->RemoveAllObservers();
|
||||
optimizer->AddObserver(itk::IterationEvent(), optimizerObserver);
|
||||
|
||||
registration->SetOptimizer(optimizer);
|
||||
} else {
|
||||
|
||||
amoebaoptimizer->SetMinimize(true);
|
||||
amoebaoptimizer->SetMaximumNumberOfIterations(100);
|
||||
amoebaoptimizer->SetParametersConvergenceTolerance(0.1);
|
||||
amoebaoptimizer->SetFunctionConvergenceTolerance(0.000002);
|
||||
|
||||
amoebaoptimizer->SetAutomaticInitialSimplex(false);
|
||||
//Initial size of the simplex (otherwise it is a very small number and optimizer stops immeditaly)
|
||||
// 2 mm / 2 degrees seems to be a good value which performs well.
|
||||
OptimizerType::ParametersType simplexDelta(3);
|
||||
int numberOfDOF = GetNumberOfDOF(dof);
|
||||
if (numberOfDOF == 0) {
|
||||
itkExceptionMacro(<< "Unkown or unsupported degree of freedom");
|
||||
}
|
||||
for (int i = 0; i < numberOfDOF; i++) {
|
||||
simplexDelta[i] = 2.0;
|
||||
}
|
||||
amoebaoptimizer->SetInitialSimplexDelta(simplexDelta);
|
||||
|
||||
amoebaoptimizer->RemoveAllObservers();
|
||||
amoebaoptimizer->AddObserver(itk::IterationEvent(), optimizerObserver);
|
||||
|
||||
registration->SetOptimizer(amoebaoptimizer);
|
||||
}
|
||||
|
||||
} else {
|
||||
//only support for 3DOF
|
||||
const int numberOfSteps = 25; //In each direction. Total number of steps is ((2*numberOfSteps+1))^3. For 25 -> 132651.
|
||||
const double stepLength = 0.1;
|
||||
|
||||
auto parameters = transform1->GetParameters();
|
||||
transform1->SetParameters(parameters);
|
||||
|
||||
ExhaustiveOptimizerType::StepsType steps(3);
|
||||
steps[0] = numberOfSteps;
|
||||
steps[1] = numberOfSteps;
|
||||
steps[2] = numberOfSteps;
|
||||
exhaustiveOptimizer->SetNumberOfSteps(steps);
|
||||
exhaustiveOptimizer->SetStepLength(stepLength);
|
||||
|
||||
exhaustiveOptimizer->RemoveAllObservers();
|
||||
exhaustiveOptimizer->AddObserver(itk::IterationEvent(), exhaustiveOptimizerObserver);
|
||||
|
||||
exhaustiveOptimizer->SetStepLength(stepLength);
|
||||
registration->SetOptimizer(exhaustiveOptimizer);
|
||||
}
|
||||
|
||||
std::cout << "#" << __COMPACT_PRETTY_FUNCTION__ << std::endl;
|
||||
}
|
||||
|
||||
int itkImageProcessor::StartRegistration(std::string extraInfo)
|
||||
{
|
||||
|
||||
std::cout << "*" << __COMPACT_PRETTY_FUNCTION__ << std::endl;
|
||||
// TODO: Check if the registartion pipeline has been initialized
|
||||
using ParametersType = RegistrationType::ParametersType;
|
||||
|
||||
auto startParameters = transform1->GetParameters();
|
||||
|
||||
time_t t = time(0); // get time now
|
||||
struct tm* now = localtime(&t);
|
||||
|
||||
bool useDumpToFile = false;
|
||||
|
||||
char buffer[255];
|
||||
strftime(buffer, 255, "test-%F-%H%M%S.txt", now);
|
||||
|
||||
std::fstream fs;
|
||||
|
||||
if (useDumpToFile || m_UseExhaustiveOptmizer) {
|
||||
fs.open(buffer, std::fstream::out);
|
||||
fs << extraInfo;
|
||||
fs << "Value\tX\tY\tZ " << std::endl;
|
||||
|
||||
if (m_UseExhaustiveOptmizer) {
|
||||
exhaustiveOptimizerObserver->set_stream(fs);
|
||||
}
|
||||
}
|
||||
|
||||
// Start the registration
|
||||
// ~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
// Create a timer to record calculation time.
|
||||
itk::TimeProbesCollectorBase timer;
|
||||
|
||||
if (verbose) {
|
||||
std::cout << "Starting the registration now..." << std::endl;
|
||||
}
|
||||
|
||||
try {
|
||||
timer.Start("Registration");
|
||||
// Start the registration.
|
||||
registration->StartRegistration();
|
||||
timer.Stop("Registration");
|
||||
} catch (itk::ExceptionObject& err) {
|
||||
std::cout << "ExceptionObject caught !" << std::endl;
|
||||
std::cout << err << std::endl;
|
||||
return -1;
|
||||
}
|
||||
|
||||
auto oldprecision = fs.precision();
|
||||
|
||||
if (m_UseExhaustiveOptmizer) {
|
||||
fs.precision(std::numeric_limits<double>::digits10 + 2);
|
||||
fs << " MinimumMetricValue: " << exhaustiveOptimizer->GetMinimumMetricValue() << std::endl;
|
||||
fs << " MaximumMetricValue: " << exhaustiveOptimizer->GetMaximumMetricValue() << std::endl;
|
||||
fs.precision(oldprecision);
|
||||
fs << " MinimumMetricValuePosition: " << exhaustiveOptimizer->GetMinimumMetricValuePosition() << std::endl;
|
||||
fs << " MaximumMetricValuePosition: " << exhaustiveOptimizer->GetMaximumMetricValuePosition() << std::endl;
|
||||
fs << " StopConditionDescription: " << exhaustiveOptimizer->GetStopConditionDescription() << std::endl;
|
||||
fs << " MaximumMetricValuePosition: " << exhaustiveOptimizer->GetMaximumMetricValuePosition() << std::endl;
|
||||
} else if (useDumpToFile) {
|
||||
fs.precision(std::numeric_limits<double>::digits10 + 2);
|
||||
fs << " FinalMetricValue: " << optimizer->GetValue() << std::endl; //same as GetCurrentCost
|
||||
fs.precision(oldprecision);
|
||||
fs << " FinalPosition: " << optimizer->GetCurrentPosition() << std::endl;
|
||||
fs << " Iterations: " << optimizer->GetCurrentIteration() << std::endl;
|
||||
fs << " StopConditionDescription: " << optimizer->GetStopConditionDescription() << std::endl;
|
||||
}
|
||||
|
||||
fs.close();
|
||||
|
||||
m_OptmizerValue = optimizer->GetValue();
|
||||
|
||||
auto finalParameters = transform1->GetParameters();
|
||||
optimizer->GetCurrentPosition();
|
||||
finalParameters = finalParameters - startParameters;
|
||||
|
||||
TransformType::Pointer offsetTransform = TransformType::New();
|
||||
offsetTransform->SetParameters(finalParameters);
|
||||
|
||||
CalculateExternalUserTransform(offsetTransform, m_DRTImage1MetaInfo);
|
||||
|
||||
const double translationAlongX = finalParameters[3];
|
||||
const double translationAlongY = finalParameters[4];
|
||||
const double translationAlongZ = finalParameters[5];
|
||||
const double rotationAlongX = finalParameters[0];
|
||||
const double rotationAlongY = finalParameters[1];
|
||||
const double rotationAlongZ = finalParameters[2];
|
||||
|
||||
const int numberOfIterations = optimizer->GetCurrentIteration();
|
||||
|
||||
std::cout << "Result = " << std::endl;
|
||||
std::cout << " Rotation Along X = " << rotationAlongX / dtr << " deg" << std::endl;
|
||||
std::cout << " Rotation Along Y = " << rotationAlongY / dtr << " deg" << std::endl;
|
||||
std::cout << " Rotation Along Z = " << rotationAlongZ / dtr << " deg" << std::endl;
|
||||
std::cout << " Translation X = " << translationAlongX << " mm" << std::endl;
|
||||
std::cout << " Translation Y = " << translationAlongY << " mm" << std::endl;
|
||||
std::cout << " Translation Z = " << translationAlongZ << " mm" << std::endl;
|
||||
std::cout << " Number Of Iterations = " << numberOfIterations << std::endl;
|
||||
std::cout << " Metric value = " << m_OptmizerValue << std::endl;
|
||||
|
||||
std::cout << "#" << __COMPACT_PRETTY_FUNCTION__ << std::endl;
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
void itkImageProcessor::InitializeProjector()
|
||||
{
|
||||
@ -2643,6 +3044,85 @@ double* itkImageProcessor::GetTransformParameters(){
|
||||
return dTransfParam;
|
||||
}
|
||||
|
||||
// Doubts about this user thing
|
||||
void itkImageProcessor::GetFinalTranslations(double& dX, double& dY, double& dZ)
|
||||
{
|
||||
ImageType3D::PointType translations = m_TransformMetaInfo->GetTranslations();
|
||||
ImageType3D::PointType userTranslations = m_TransformMetaInfo->GetUserTranslations();
|
||||
|
||||
dX = translations[0] + userTranslations[0];
|
||||
dY = translations[1] + userTranslations[1];
|
||||
dZ = translations[2] + userTranslations[2];
|
||||
}
|
||||
|
||||
void itkImageProcessor::GetFinalRotations(double& dRX, double& dRY, double& dRZ)
|
||||
{
|
||||
ImageType3D::PointType rotations = m_TransformMetaInfo->GetRotations();
|
||||
ImageType3D::PointType userRotations = m_TransformMetaInfo->GetUserRotations();
|
||||
|
||||
dRX = rotations[0] + userRotations[0];
|
||||
dRY = rotations[1] + userRotations[1];
|
||||
dRZ = rotations[2] + userRotations[2];
|
||||
}
|
||||
|
||||
|
||||
double itkImageProcessor::GetOptimizerValue()
|
||||
{
|
||||
return m_OptmizerValue;
|
||||
}
|
||||
|
||||
double itkImageProcessor::GetCurrentMetricValue()
|
||||
{
|
||||
//Note: this fails if the metric has not been propperly initilzed.
|
||||
|
||||
if (!m_UseMutualInformation) {
|
||||
if (metric == NULL) {
|
||||
return nan("");
|
||||
}
|
||||
return metric->GetValue();
|
||||
} else {
|
||||
if (mimetric == NULL) {
|
||||
return nan("");
|
||||
}
|
||||
return mimetric->GetValue();
|
||||
}
|
||||
}
|
||||
|
||||
void itkImageProcessor::SetROI(double, double, double, double)
|
||||
{
|
||||
//TODO: Not implemanted yet. ROI are hard coded and can be enabled using SetFullROI.
|
||||
}
|
||||
|
||||
void itkImageProcessor::SetOptimizer(std::string optimizer)
|
||||
{
|
||||
if (optimizer.compare("Powell") == 0) {
|
||||
m_UseAmeobaOptimizer = false;
|
||||
m_UseExhaustiveOptmizer = false;
|
||||
} else if (optimizer.compare("Amoeba") == 0) {
|
||||
m_UseExhaustiveOptmizer = false;
|
||||
m_UseAmeobaOptimizer = true;
|
||||
} else if (optimizer.compare("Exhaustive") == 0) {
|
||||
m_UseExhaustiveOptmizer = true;
|
||||
m_UseAmeobaOptimizer = false;
|
||||
} else {
|
||||
itkExceptionMacro(<< "Unkown optimzer string : " << optimizer);
|
||||
}
|
||||
}
|
||||
void itkImageProcessor::SetMetric(std::string metric)
|
||||
{
|
||||
if (metric.compare("NCC") == 0) {
|
||||
m_UseMutualInformation = false;
|
||||
} else if (metric.compare("MI") == 0) {
|
||||
m_UseMutualInformation = true;
|
||||
} else {
|
||||
itkExceptionMacro(<< "Unkown metric string : " << optimizer);
|
||||
}
|
||||
}
|
||||
void itkImageProcessor::SetFullROI(bool fullROI)
|
||||
{
|
||||
m_UseFullROI = fullROI;
|
||||
// TODO: Remove this function when ROI functinalitz has been implemented.
|
||||
}
|
||||
|
||||
} // end namespace itk
|
||||
|
||||
|
||||
@ -30,6 +30,13 @@ gfattori 08.11.2021
|
||||
#include "itkObjectFactory.h"
|
||||
#include "itkSmartPointer.h"
|
||||
|
||||
#include "itkExhaustiveOptimizer.h"
|
||||
#include "itkMutualInformationTwoImageToOneImageMetric.h"
|
||||
#include "itkNormalizedCorrelationTwoImageToOneImageMetric.h"
|
||||
#include "itkPowellOptimizer.h"
|
||||
#include "itkTwoProjectionImageRegistrationMethod.h"
|
||||
#include "itkAmoebaOptimizer.h"
|
||||
|
||||
#include "itkImageToVTKImageFilter.h"
|
||||
|
||||
#include "itkImageFileReader.h"
|
||||
@ -46,13 +53,104 @@ gfattori 08.11.2021
|
||||
|
||||
namespace itk
|
||||
{
|
||||
/* reference string required for comparison with tag values */
|
||||
static const char *ImageOrientationStrings[] = {
|
||||
"NotDefined",
|
||||
"HFS",
|
||||
"FFS"
|
||||
|
||||
class CommandIterationUpdate : public itk::Command {
|
||||
// TODO: Move to own files.
|
||||
|
||||
public:
|
||||
using Self = CommandIterationUpdate;
|
||||
using Superclass = itk::Command;
|
||||
using Pointer = itk::SmartPointer<Self>;
|
||||
itkNewMacro(Self);
|
||||
|
||||
protected:
|
||||
CommandIterationUpdate() = default;
|
||||
|
||||
public:
|
||||
using OptimizerType = itk::PowellOptimizer;
|
||||
using OptimizerPointer = const OptimizerType*;
|
||||
|
||||
using AmoebaOptimizerType = itk::AmoebaOptimizer;
|
||||
;
|
||||
using AmoebaOptimizerPointer = const OptimizerType*;
|
||||
|
||||
void
|
||||
Execute(itk::Object* caller, const itk::EventObject& event) override
|
||||
{
|
||||
Execute((const itk::Object*)caller, event);
|
||||
}
|
||||
|
||||
void
|
||||
Execute(const itk::Object* object, const itk::EventObject& event) override
|
||||
{
|
||||
auto optimizer = dynamic_cast<OptimizerPointer>(object);
|
||||
if (typeid(event) == typeid(itk::IterationEvent)) {
|
||||
|
||||
//Feedback from the optimizer executed at the end of every itteration
|
||||
// currently just print the result into the cout. We might add
|
||||
// functionality to register and emit signals to update the UI.
|
||||
|
||||
std::cout << "Iteration: " << optimizer->GetCurrentIteration() << std::endl;
|
||||
auto oldprecision = std::cout.precision();
|
||||
std::cout.precision(std::numeric_limits<double>::digits10 + 2);
|
||||
std::cout << "Similarity: " << optimizer->GetValue() << std::endl;
|
||||
std::cout.precision(oldprecision);
|
||||
std::cout << "Position: " << optimizer->GetCurrentPosition() << std::endl;
|
||||
}
|
||||
return;
|
||||
}
|
||||
};
|
||||
|
||||
class ExhaustiveCommandIterationUpdate : public itk::Command {
|
||||
// TODO: Move to own files.
|
||||
|
||||
public:
|
||||
using Self = ExhaustiveCommandIterationUpdate;
|
||||
using Superclass = itk::Command;
|
||||
using Pointer = itk::SmartPointer<Self>;
|
||||
itkNewMacro(Self);
|
||||
|
||||
std::ostream* os;
|
||||
|
||||
protected:
|
||||
ExhaustiveCommandIterationUpdate() = default;
|
||||
|
||||
public:
|
||||
using OptimizerType = itk::ExhaustiveOptimizer;
|
||||
;
|
||||
using OptimizerPointer = const OptimizerType*;
|
||||
|
||||
void set_stream(std::ostream& stream)
|
||||
{
|
||||
os = &stream;
|
||||
}
|
||||
|
||||
void
|
||||
Execute(itk::Object* caller, const itk::EventObject& event) override
|
||||
{
|
||||
Execute((const itk::Object*)caller, event);
|
||||
}
|
||||
|
||||
void
|
||||
Execute(const itk::Object* object, const itk::EventObject& event) override
|
||||
{
|
||||
auto optimizer = dynamic_cast<OptimizerPointer>(object);
|
||||
if (typeid(event) == typeid(itk::IterationEvent)) {
|
||||
|
||||
//crude LPS to IEC transform for HFS.
|
||||
auto position = optimizer->GetCurrentPosition();
|
||||
|
||||
auto oldprecision = os->precision();
|
||||
os->precision(std::numeric_limits<double>::digits10 + 2);
|
||||
*os << optimizer->GetCurrentValue();
|
||||
os->precision(oldprecision);
|
||||
*os << "\t" << position[0] << "\t" << position[2] << "\t" << -position[1] << std::endl;
|
||||
}
|
||||
return;
|
||||
}
|
||||
};
|
||||
|
||||
|
||||
class ITK_EXPORT itkImageProcessor : public itk::Object
|
||||
{
|
||||
|
||||
@ -97,6 +195,10 @@ public:
|
||||
double GetSCD1();
|
||||
double GetSCD2();
|
||||
|
||||
/** Sets the degree of freedom for omptimzation*/
|
||||
void SetDegreeOfFreedom(tDegreeOfFreedomEnum);
|
||||
tDegreeOfFreedomEnum GetDegreeOfFreedom();
|
||||
|
||||
void SetCustom_ProjectionCenterOffsetFixedAxes_IEC(double,double,double,double,double,double);
|
||||
|
||||
void SetCustom_ProjectionCenterFixedAxes_IEC(double,double,double);
|
||||
@ -117,6 +219,19 @@ public:
|
||||
void SetInitialTranslations(double, double, double);
|
||||
void SetInitialRotations(double, double, double);
|
||||
|
||||
/** Get transform parameters for 3D Volume */
|
||||
void GetFinalTranslations(double&, double&, double&);
|
||||
void GetFinalRotations(double&, double&, double&);
|
||||
|
||||
/** Set user transform parameters for 3D Volume in LPS*/
|
||||
void SetUserTranslationsLPS(double, double, double);
|
||||
void SetUserRotationsLPS(double, double, double);
|
||||
|
||||
/** Initialize the registration pipeline*/
|
||||
void InitializeRegistration(int, double, double, eDegreeOfFreedomType);
|
||||
/** Start the registration process*/
|
||||
int StartRegistration(std::string extraInfo);
|
||||
|
||||
/** Get transform parameters for 3D Volume */
|
||||
double* GetTransformParameters();
|
||||
|
||||
@ -129,8 +244,6 @@ public:
|
||||
/** Get Projection origin in LPS coordinates*/
|
||||
const std::vector <double> GetRTImportOffset();
|
||||
|
||||
|
||||
|
||||
/** Get the Localizer intensity window and
|
||||
* center for rendering */
|
||||
double GetLocalizerDisplayWindowLevel(int );
|
||||
@ -153,6 +266,17 @@ public:
|
||||
void WriteProjectionImages();
|
||||
void Write2DImages();
|
||||
|
||||
/** Get the current cost function value from the optimizer*/
|
||||
double GetOptimizerValue();
|
||||
|
||||
/** Get the cost function value for the current transform*/
|
||||
double GetCurrentMetricValue();
|
||||
|
||||
void SetROI(double, double, double, double);
|
||||
|
||||
void SetOptimizer(std::string);
|
||||
void SetMetric(std::string);
|
||||
void SetFullROI(bool);
|
||||
|
||||
|
||||
protected:
|
||||
@ -189,6 +313,16 @@ private:
|
||||
using InterpolatorType = itk::gSiddonJacobsRayCastInterpolateImageFunction<InternalImageType, double>;
|
||||
using ResampleFilterType = itk::ResampleImageFilter<InternalImageType, InternalImageType>;
|
||||
|
||||
/** Optimizer which tries to find the minimn (Powell Optimizer)*/
|
||||
using OptimizerType = itk::PowellOptimizer;
|
||||
using AmoebaOptimizerType = itk::AmoebaOptimizer;
|
||||
/** Optimizer which samples the whol space */
|
||||
using ExhaustiveOptimizerType = itk::ExhaustiveOptimizer;
|
||||
/** Metric to calculate similarites between images*/
|
||||
using MetricType = itk::NormalizedCorrelationTwoImageToOneImageMetric<InternalImageType, InternalImageType>;
|
||||
using MIMetricType = itk::MutualInformationTwoImageToOneImageMetric<InternalImageType, InternalImageType>;
|
||||
/** The thing which actuall does the image registration*/
|
||||
using RegistrationType = itk::TwoProjectionImageRegistrationMethod<InternalImageType, InternalImageType>;
|
||||
|
||||
/** Image reader types */
|
||||
using ImageReaderType2D = itk::ImageFileReader<ImageType2D>;
|
||||
@ -206,6 +340,8 @@ private:
|
||||
/** ITK to VTK filter */
|
||||
using ITKtoVTKFilterType = itk::ImageToVTKImageFilter<OutputImageType>;
|
||||
|
||||
void
|
||||
CalculateExternalUserTransform(TransformType::Pointer transform, DRTImageMetaInformation::Pointer imageMetaInfo);
|
||||
|
||||
TransformType::Pointer
|
||||
CalculateInternalTransform(
|
||||
@ -239,6 +375,23 @@ private:
|
||||
imageDRT1In,
|
||||
imageDRT2In;
|
||||
|
||||
RegistrationType::Pointer
|
||||
registration;
|
||||
MetricType::Pointer
|
||||
metric;
|
||||
MIMetricType::Pointer
|
||||
mimetric;
|
||||
OptimizerType::Pointer
|
||||
optimizer;
|
||||
AmoebaOptimizerType::Pointer
|
||||
amoebaoptimizer;
|
||||
CommandIterationUpdate::Pointer
|
||||
optimizerObserver;
|
||||
ExhaustiveOptimizerType::Pointer
|
||||
exhaustiveOptimizer;
|
||||
ExhaustiveCommandIterationUpdate::Pointer
|
||||
exhaustiveOptimizerObserver;
|
||||
|
||||
DuplicatorType::Pointer
|
||||
m_LATSourceDupli,
|
||||
m_PASourceDupli,
|
||||
@ -335,6 +488,15 @@ private:
|
||||
TransformMetaInformation::Pointer
|
||||
m_TransformMetaInfo;
|
||||
|
||||
|
||||
double m_OptmizerValue;
|
||||
|
||||
bool m_UseExhaustiveOptmizer;
|
||||
bool m_UseAmeobaOptimizer;
|
||||
bool m_UseFullROI;
|
||||
bool m_UseMutualInformation;
|
||||
bool m_UseDumptoFile;
|
||||
|
||||
};
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user