fattori_g/reg23Topograms
0
0
Fork 0
Code Issues 1 Pull Requests Actions Packages Projects Releases Wiki Activity

Review of multiple optimizers - metrics

Browse Source 
- not usuable util the opti and metric types are better defined using enums
- ROI are passed to both metrics
- Full functionalty only for Powell(NCC or MI), mainly due to GetFinalR23Parameters which get those from Powell....
This commit is contained in:
Proton local user
2023-05-17 23:53:02 +02:00
parent ab29d81e5e
commit d67627a6fc
5 changed files with 138 additions and 93 deletions
Download Patch File Download Diff File Expand all files Collapse all files

3
reg23Topograms/itkDTRrecon/autoreg/CMakeLists.txt
View File

@ -1,6 +1,5 @@
SET(LIB_NAME autoreg)
SET(CMAKE_CXX_FLAGS "-std=c++11 -fPIC")
#SET(CMAKE_CXX_FLAGS "-std=c++11 -fPIC")
find_package(ITK REQUIRED)
include(${ITK_USE_FILE})

6
reg23Topograms/itkDTRrecon/autoreg/itkMutualInformationTwoImageToOneImageMetric.hxx
View File

@ -149,6 +149,12 @@ MutualInformationTwoImageToOneImageMetric<TFixedImage, TMovingImage>::GetValue()
//metric1->UseAllPixelsOn();
metric1->SetNumberOfHistogramBins(50);
// InternalImageType::IndexType pIndex;
// pIndex[0]=200;
// pIndex[1]=300;
// InternalImageType::PixelType pPixel = fixedImage1->GetPixel(pIndex);
// std::cout<<"MATTES PIXEL: "<<pPixel <<std::endl;
metric1->SetFixedImage(fixedImage1);
metric1->SetMovingImage(this->m_Filter1->GetOutput());

1
reg23Topograms/itkDTRrecon/autoreg/itkNormalizedCorrelationTwoImageToOneImageMetric.hxx
View File

@ -76,7 +76,6 @@ NormalizedCorrelationTwoImageToOneImageMetric<TFixedImage, TMovingImage>::Calcul
this->m_NumberOfPixelsCounted = 0;
int numberOfPixelsVisited = 0;
//filter->Update();
filter->Update();
MovingImageConstPointer imageDRTIn = filter->GetOutput();
//this->WriteImage(imageDRTIn, "", "");

203
reg23Topograms/itkDTRrecon/itkImageProcessor.cpp
View File

@ -142,37 +142,38 @@ itkImageProcessor::itkImageProcessor()
m_DRTGeometryMetaInfo->SetProjectionCenterOffset2(Point3D);
// setup the Automatic Registration
metric = MetricType::New();
mimetric = MIMetricType::New();
optimizer = OptimizerType::New();
NCCmetric = MetricType::New();
MImetric = MIMetricType::New();
PowellOptimizer = PowellOptimizerType::New();
amoebaoptimizer = AmoebaOptimizerType::New();
AmoebaOptimizer = AmoebaOptimizerType::New();
optimizerObserver = CommandIterationUpdate::New();
exhaustiveOptimizer = ExhaustiveOptimizerType::New();
exhaustiveOptimizerObserver = ExhaustiveCommandIterationUpdate::New();
ExhaustiveOptimizer = ExhaustiveOptimizerType::New();
ExhaustiveOptimizerObserver = ExhaustiveCommandIterationUpdate::New();
registration = RegistrationType::New();
optimizerObserver->SetProcess(registration);
if (m_UseMutualInformation) {
registration->SetMetric(mimetric);
} else {
registration->SetMetric(metric);
}
/* default is MI */
m_UseMutualInformation = true; //oterwise NCC is used
registration->SetMetric(MImetric);
/* default is Powell */
m_UseExhaustiveOptmizer = false; //if the exhaustive optimizer shal be used, ovverrides ameoba
m_UseAmeobaOptimizer = false; //if the ameoba optimzer shall be used, otherwise Powell. Overriden by Exhaustive option.
registration->SetOptimizer(PowellOptimizer);
registration->SetOptimizer(optimizer);
registration->SetTransform1(transform1);
registration->SetTransform2(transform2);
registration->SetInterpolator1(interpolator1);
registration->SetInterpolator2(interpolator2);
m_UseExhaustiveOptmizer = false; //if the exhaustive optimizer shal be used, ovverrides ameoba
m_UseAmeobaOptimizer = false; //if the ameoba optimzer shall be used, otherwise Powell. Overriden by Exhaustive option.
m_UseFullROI = true; // if the full image ROI shall be used
m_UseMutualInformation = false; //oterwise NCC is used
m_UseDumptoFile = false; //If each (!) optimzer result shall be dumpped into a file.
}
itkImageProcessor::~itkImageProcessor()
@ -1031,7 +1032,12 @@ int itkImageProcessor::load2D(const char * pcFName){
m_Duplicator->SetInputImage(caster2DInput->GetOutput() );
m_Duplicator->Update();
InternalImageType::IndexType pIndex;
pIndex[0]=200;
pIndex[1]=300;
InternalImageType::PixelType pPixel =
m_Duplicator->GetOutput()->GetPixel(pIndex);
std::cout<<"processro PIXEL: "<<pPixel <<std::endl;
// std::cout<< " ////////////// 2D Topo BEG " <<std::endl;
// std::cout<<"GetDirection()"<<m_Duplicator->GetOutput()->GetDirection()<<std::endl;
@ -1153,18 +1159,20 @@ void itkImageProcessor::InitializeRegistration(
itkExceptionMacro(<< "CT data not present");
}
metric->ComputeGradientOff();
metric->SetSubtractMean(true);
metric->SetMaxTranslation(maxTranslation);
NCCmetric->ComputeGradientOff();
MImetric->ComputeGradientOff();
NCCmetric->SetSubtractMean(true);
NCCmetric->SetMaxTranslation(maxTranslation);
MImetric->SetMaxTranslation(maxTranslation);
// m_TransformMetaInfo->SetDegreeOfFreedom(dof);
m_r23MetaInfo->SetDegreeOfFreedom(dof);
mimetric->ComputeGradientOff();
if (verbose) {
metric->DebugOn();
NCCmetric->DebugOn();
MImetric->DebugOn();
}
@ -1184,8 +1192,10 @@ void itkImageProcessor::InitializeRegistration(
registration->SetFixedImageRegion1(roiAutoReg1);
registration->SetFixedImageRegion2(roiAutoReg2);
mimetric->SetFixedImageRegion1(roiAutoReg1);
mimetric->SetFixedImageRegion2(roiAutoReg2);
MImetric->SetFixedImageRegion1(roiAutoReg1);
MImetric->SetFixedImageRegion2(roiAutoReg2);
NCCmetric->SetFixedImageRegion1(roiAutoReg1);
NCCmetric->SetFixedImageRegion2(roiAutoReg2);
std::cout << "using ROIs for Auto Reg " << std::endl;
@ -1201,8 +1211,10 @@ void itkImageProcessor::InitializeRegistration(
registration->SetFixedImageRegion1(region1);
registration->SetFixedImageRegion2(region2);
mimetric->SetFixedImageRegion1(roiAutoReg1);
mimetric->SetFixedImageRegion2(roiAutoReg2);
MImetric->SetFixedImageRegion1(roiAutoReg1);
MImetric->SetFixedImageRegion2(roiAutoReg2);
NCCmetric->SetFixedImageRegion1(roiAutoReg1);
NCCmetric->SetFixedImageRegion2(roiAutoReg2);
}
@ -1244,35 +1256,35 @@ void itkImageProcessor::InitializeRegistration(
// 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(m_MaxNumberOfIterations);
optimizer->SetMaximumLineIteration(4); // for Powell's method
optimizer->SetStepLength(stepLength);
optimizer->SetStepTolerance(0.01);
optimizer->SetValueTolerance(0.000002);
PowellOptimizer->SetMaximize(false); // for NCC and MI
PowellOptimizer->SetMaximumIteration(m_MaxNumberOfIterations);
PowellOptimizer->SetMaximumLineIteration(4); // for Powell's method
PowellOptimizer->SetStepLength(stepLength);
PowellOptimizer->SetStepTolerance(0.01);
PowellOptimizer->SetValueTolerance(0.000002);
if (verbose) {
optimizer->DebugOn();
optimizer->Print(std::cout);
PowellOptimizer->DebugOn();
PowellOptimizer->Print(std::cout);
}
optimizer->RemoveAllObservers();
optimizer->AddObserver(itk::AnyEvent(), optimizerObserver);
PowellOptimizer->RemoveAllObservers();
PowellOptimizer->AddObserver(itk::AnyEvent(), optimizerObserver);
registration->SetOptimizer(optimizer);
registration->SetOptimizer(PowellOptimizer);
registration->RemoveAllObservers();
} else {
amoebaoptimizer->SetMinimize(true);
amoebaoptimizer->SetMaximumNumberOfIterations(100);
amoebaoptimizer->SetParametersConvergenceTolerance(0.1);
amoebaoptimizer->SetFunctionConvergenceTolerance(0.000002);
AmoebaOptimizer->SetMinimize(true);
AmoebaOptimizer->SetMaximumNumberOfIterations(100);
AmoebaOptimizer->SetParametersConvergenceTolerance(0.1);
AmoebaOptimizer->SetFunctionConvergenceTolerance(0.000002);
amoebaoptimizer->SetAutomaticInitialSimplex(false);
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);
AmoebaOptimizerType::ParametersType simplexDelta(3);
int numberOfDOF = GetNumberOfDOF(dof);
if (numberOfDOF == 0) {
itkExceptionMacro(<< "Unkown or unsupported degree of freedom");
@ -1280,12 +1292,12 @@ void itkImageProcessor::InitializeRegistration(
for (int i = 0; i < numberOfDOF; i++) {
simplexDelta[i] = 2.0;
}
amoebaoptimizer->SetInitialSimplexDelta(simplexDelta);
AmoebaOptimizer->SetInitialSimplexDelta(simplexDelta);
amoebaoptimizer->RemoveAllObservers();
amoebaoptimizer->AddObserver(itk::IterationEvent(), optimizerObserver);
AmoebaOptimizer->RemoveAllObservers();
AmoebaOptimizer->AddObserver(itk::IterationEvent(), optimizerObserver);
registration->SetOptimizer(amoebaoptimizer);
registration->SetOptimizer(AmoebaOptimizer);
}
} else {
@ -1300,14 +1312,14 @@ void itkImageProcessor::InitializeRegistration(
steps[0] = numberOfSteps;
steps[1] = numberOfSteps;
steps[2] = numberOfSteps;
exhaustiveOptimizer->SetNumberOfSteps(steps);
exhaustiveOptimizer->SetStepLength(stepLength);
ExhaustiveOptimizer->SetNumberOfSteps(steps);
ExhaustiveOptimizer->SetStepLength(stepLength);
exhaustiveOptimizer->RemoveAllObservers();
exhaustiveOptimizer->AddObserver(itk::IterationEvent(), exhaustiveOptimizerObserver);
ExhaustiveOptimizer->RemoveAllObservers();
ExhaustiveOptimizer->AddObserver(itk::IterationEvent(), ExhaustiveOptimizerObserver);
exhaustiveOptimizer->SetStepLength(stepLength);
registration->SetOptimizer(exhaustiveOptimizer);
ExhaustiveOptimizer->SetStepLength(stepLength);
registration->SetOptimizer(ExhaustiveOptimizer);
}
std::cout << "#" << __COMPACT_PRETTY_FUNCTION__ << std::endl;
@ -1338,7 +1350,7 @@ int itkImageProcessor::StartRegistration(std::string extraInfo)
fs << "Value\tX\tY\tZ " << std::endl;
if (m_UseExhaustiveOptmizer) {
exhaustiveOptimizerObserver->set_stream(fs);
ExhaustiveOptimizerObserver->set_stream(fs);
}
}
@ -1369,31 +1381,48 @@ int itkImageProcessor::StartRegistration(std::string extraInfo)
if (m_UseExhaustiveOptmizer) {
fs.precision(std::numeric_limits<double>::digits10 + 2);
fs << " MinimumMetricValue: " << exhaustiveOptimizer->GetMinimumMetricValue() << std::endl;
fs << " MaximumMetricValue: " << exhaustiveOptimizer->GetMaximumMetricValue() << std::endl;
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;
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 << " FinalMetricValue: " << PowellOptimizer->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 << " FinalPosition: " << PowellOptimizer->GetCurrentPosition() << std::endl;
fs << " Iterations: " << PowellOptimizer->GetCurrentIteration() << std::endl;
fs << " StopConditionDescription: " << PowellOptimizer->GetStopConditionDescription() << std::endl;
}
fs.close();
m_OptmizerValue = optimizer->GetValue();
auto finalParameters = optimizer->GetCurrentPosition();
m_OptmizerValue = PowellOptimizer->GetValue();
if(!m_UseExhaustiveOptmizer){
if(!m_UseAmeobaOptimizer){
//Powell
auto finalParameters = PowellOptimizer->GetCurrentPosition();
std::cout<<"REG FINAL PARS: "<<finalParameters<<std::endl;
}else{
//Amoeba
auto finalParameters = AmoebaOptimizer->GetCurrentPosition();
std::cout<<"REG FINAL PARS: "<<finalParameters<<std::endl;
}
}else{
//use exhaustive
auto finalParameters = ExhaustiveOptimizer->GetCurrentPosition();
std::cout<<"REG FINAL PARS: "<<finalParameters<<std::endl;
}
// auto finalParameters = transform1->GetParameters();
// std::cout<<"-->startParameters "<<startParameters<<std::endl;
@ -1452,32 +1481,32 @@ itkImageProcessor::GetFinalR23Parameters(){
Optimizer::ParametersType pPars(6);
pPars.fill(0.);
if(optimizer == nullptr){
if(PowellOptimizer == nullptr){
return pPars;
}
switch (m_r23MetaInfo->GetDegreeOfFreedom()) {
case THREE_DOF:
pPars[3] = optimizer->GetCurrentPosition()[0]
pPars[3] = PowellOptimizer->GetCurrentPosition()[0]
- m_TransformMetaInfo->GetHiddenTranslations()[0];
pPars[4] = optimizer->GetCurrentPosition()[1]
pPars[4] = PowellOptimizer->GetCurrentPosition()[1]
- m_TransformMetaInfo->GetHiddenTranslations()[1];
pPars[5] = optimizer->GetCurrentPosition()[2]
pPars[5] = PowellOptimizer->GetCurrentPosition()[2]
- m_TransformMetaInfo->GetHiddenTranslations()[2];
break;
case SIX_DOF:
pPars[0] = optimizer->GetCurrentPosition()[0]
pPars[0] = PowellOptimizer->GetCurrentPosition()[0]
- m_TransformMetaInfo->GetHiddenRotations()[0];
pPars[1] = optimizer->GetCurrentPosition()[1]
pPars[1] = PowellOptimizer->GetCurrentPosition()[1]
- m_TransformMetaInfo->GetHiddenRotations()[1];
pPars[2] = optimizer->GetCurrentPosition()[2]
pPars[2] = PowellOptimizer->GetCurrentPosition()[2]
- m_TransformMetaInfo->GetHiddenRotations()[2];
pPars[3] = optimizer->GetCurrentPosition()[3]
pPars[3] = PowellOptimizer->GetCurrentPosition()[3]
- m_TransformMetaInfo->GetHiddenTranslations()[0];
pPars[4] = optimizer->GetCurrentPosition()[4]
pPars[4] = PowellOptimizer->GetCurrentPosition()[4]
- m_TransformMetaInfo->GetHiddenTranslations()[1];
pPars[5] = optimizer->GetCurrentPosition()[5]
pPars[5] = PowellOptimizer->GetCurrentPosition()[5]
- m_TransformMetaInfo->GetHiddenTranslations()[2];
break;
@ -2776,15 +2805,15 @@ double itkImageProcessor::GetCurrentMetricValue()
//Note: this fails if the metric has not been propperly initilzed.
if (!m_UseMutualInformation) {
if (metric == NULL) {
if (NCCmetric == NULL) {
return nan("");
}
return metric->GetValue();
return NCCmetric->GetValue();
} else {
if (mimetric == NULL) {
if (MImetric == NULL) {
return nan("");
}
return mimetric->GetValue();
return MImetric->GetValue();
}
}
@ -2794,15 +2823,20 @@ void itkImageProcessor::SetOptimizer(std::string optimizer)
if (optimizer.compare("Powell") == 0) {
m_UseAmeobaOptimizer = false;
m_UseExhaustiveOptmizer = false;
registration->SetOptimizer(PowellOptimizer);
} else if (optimizer.compare("Amoeba") == 0) {
m_UseExhaustiveOptmizer = false;
m_UseAmeobaOptimizer = true;
registration->SetOptimizer(AmoebaOptimizer);
} else if (optimizer.compare("Exhaustive") == 0) {
m_UseExhaustiveOptmizer = true;
m_UseAmeobaOptimizer = false;
registration->SetOptimizer(ExhaustiveOptimizer);
} else {
itkExceptionMacro(<< "Unkown optimzer string : " << optimizer);
}
}
void itkImageProcessor::SetMetric(std::string metric)
{
@ -2811,8 +2845,15 @@ void itkImageProcessor::SetMetric(std::string metric)
} else if (metric.compare("MI") == 0) {
m_UseMutualInformation = true;
} else {
itkExceptionMacro(<< "Unkown metric string : " << optimizer);
itkExceptionMacro(<< "Unkown metric string : " << metric);
}
if (m_UseMutualInformation) {
registration->SetMetric(this->MImetric);
} else {
registration->SetMetric(this->NCCmetric);
}
}
void itkImageProcessor::SetFullROI(bool fullROI)
{

16
reg23Topograms/itkDTRrecon/itkImageProcessor.h
View File

@ -269,7 +269,7 @@ private:
using ResampleFilterType = itk::ResampleImageFilter<InternalImageType, InternalImageType>;
/** Optimizer which tries to find the minimun (Powell Optimizer)*/
using OptimizerType = itk::PowellOptimizer;
using PowellOptimizerType = itk::PowellOptimizer;
/** Optimizer which tries to find the minimn (Powell Optimizer)*/
using AmoebaOptimizerType = itk::AmoebaOptimizer;
/** Optimizer which samples the whol space */
@ -321,17 +321,17 @@ private:
RegistrationType::Pointer
registration;
MetricType::Pointer
metric;
NCCmetric;
MIMetricType::Pointer
mimetric;
OptimizerType::Pointer
optimizer;
MImetric;
PowellOptimizerType::Pointer
PowellOptimizer;
AmoebaOptimizerType::Pointer
amoebaoptimizer;
AmoebaOptimizer;
ExhaustiveOptimizerType::Pointer
exhaustiveOptimizer;
ExhaustiveOptimizer;
ExhaustiveCommandIterationUpdate::Pointer
exhaustiveOptimizerObserver;
ExhaustiveOptimizerObserver;
DuplicatorType::Pointer
m_LATSourceDupli,